Non synonimous mutations found in sample: CIQ2J

(1)

Non synonimous mutations found in sample: CIQ2J

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 28902 . G A

A missense_variant MODERATE dapB b0031 transcript AAC73142.1 Coding 1/1 c.529G>A p.Ala177Thr 529/822 529/822 177/273 U00096 gene 28374-

29195

+ dapB b0031 JW0029 EcoGene:EG10206

U00096 CDS 28374- 29195

+ dapB b0031 JW0029 EcoGene:EG10206 enzyme; Amino acid biosynthesis: Lysine GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009089 - lysine biosynthetic process via diaminopimelate 1 11 dihydrodipicolinate reductase AAC73142.1 1.17.1.8

SAMPLE QUAL FILTER DP RPB AF1 AC1 DP4 MQ FQ PV4 VDB IS FORMAT VALUES

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 42 5.441463e-02 0.5 1 6,7,14,15 60 195 1,0.22,1,0.3 2.162466e-01 GT:PL:GQ 0/1:255,0,222:99

2 CHROM POS ID REF ALT U00096 65122 . A C

C missense_variant MODERATE polB b0060 transcript AAC73171.1 Coding 1/1 c.659T>G p.Ile220Ser 659/2352 659/2352 220/783 U00096 gene 63429-

65780

- polB b0060 JW0059 EcoGene:EG10747

U00096 CDS 63429- 65780

- polB b0060 JW0059 EcoGene:EG10747 enzyme; DNA - replication, repair, restriction/modification GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication; GO_process: GO:0006281 - DNA repair; GO_process: GO:0009314 - response to radiation; GO_process: GO:0009432 - SOS response 1 11 DNA polymerase II AAC73171.1 2.7.7.7

RESULTS_dnaQ

RESULTS_CIQ2J 222.0 . 35 1 2 0,0,21,14 60 -132 2.867278e-01 GT:PL:GQ 1/1:255,105,0:99

3 ^CHROM ^POS ^{ID REF ALT}

U00096 111731 . T C

C missense_variant MODERATE yacG b0101 transcript AAC73212.1 Coding 1/1 c.116A>G p.Glu39Gly 116/198 116/198 39/65

C downstream_gene_variant MODIFIER zapD b0102 transcript AAC73213.1 Coding c.*744A>G 125

U00096 gene 111649-111846 - yacG b0101 JW5008 EcoGene:EG12314

U00096 CDS 111649-111846 - yacG b0101 JW5008 EcoGene:EG12314 1 11 DNA gyrase inhibitor AAC73212.1

RESULTS_dnaQ

4 ^CHROM ^POS ^{ID REF ALT}

U00096 167914 . TG T

frameshift_variant HIGH fhuA b0150 transcript AAC73261.1 Coding 1/1 c.432delG p.Leu144fs 432/2244 432/2244 144/747 U00096 gene 167484-

169727

+ fhuA b0150 tonA EcoGene:EG10302

U00096 CDS 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302 membrane; Outer membrane constituents outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0009279 - cell outer membrane 1 11 ferrichrome outer membrane transporter AAC73261.1

RESULTS_dnaQ

RESULTS_CIQ2J 214.0 . 37 1 2 0,0,17,17 60 -137 5.141550e-02 33,0.891892 GT:PL:GQ 1/1:255,102,0:99

5 ^CHROM ^POS ^{ID REF ALT}

U00096 167915 . G T,C

T missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.432G>T p.Leu144Phe 432/2244 432/2244 144/747 C missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.432G>C p.Leu144Phe 432/2244 432/2244 144/747

U00096 gene 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302

(2)

U00096 CDS 167484- 169727

+ fhuA b0150 tonA EcoGene:EG10302 membrane; Outer membrane constituents outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0009279 - cell outer membrane 1 11 ferrichrome outer membrane transporter AAC73261.1

RESULTS_dnaQ

RESULTS_CIQ2J 30.8 . 4 1 2 0,0,1,3 60 -33 1.165196e-02 GT:PL:GQ 1/1:122,66,60,64,0,58:10

6 ^CHROM ^POS ^{ID REF ALT}

U00096 181536 . C G

G missense_variant MODERATE degP b0161 transcript AAC73272.1 Coding 1/1 c.653C>G p.Ala218Gly 653/1425 653/1425 218/474 U00096 gene 180884-

182308

+ degP b0161 ptd EcoGene:EG10463

U00096 CDS 180884- 182308

+ degP b0161 ptd EcoGene:EG10463 enzyme; Degradation of proteins, peptides, glycopeptides periplasmic serine protease Do; heat shock protein HtrA; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0009266 - response to temperature stimulus 1 11 serine endoprotease (protease Do), membrane-associated AAC73272.1 3.4.21.-

RESULTS_dnaQ

7 ^CHROM ^POS ^{ID REF ALT}

U00096 271123 . A T

T missense_variant MODERATE insI1 b0256 transcript AAC73359.1 Coding 1/1 c.521A>T p.Tyr174Phe 521/1152 521/1152 174/383

T intron_variant MODIFIER insN b4587 transcript b4587 Coding 1/1 c.258+588A>T WARNING_TRANSCRIPT_NO_STOP_CODON U00096 gene 270603-

271754

+ insI1 b0256 ECK0258 EcoGene:EG40009

U00096 CDS 270603- 271754

+ insI1 b0256 ECK0258 EcoGene:EG40009 IS, phage, Tn; Transposon-related functions; extrachromosomal; transposon related 1 11 IS30 transposase AAC73359.1

RESULTS_dnaQ

RESULTS_CIQ2J 28.1 . 31 1.893095e+00 1 2 5,4,18,4 11 -46 0.18,0.18,1,1 1.280277e-01 GT:PL:GQ 1/1:61,19,0:35

8 ^CHROM ^POS ^{ID REF ALT}

U00096 284582 . T G

G missense_variant MODERATE yagF b0269 transcript AAC73372.1 Coding 1/1 c.1382T>G p.Val461Gly 1382/1968 1382/1968 461/655 U00096 gene 283201-

285168

+ yagF b0269 JW0262 EcoGene:EG13345

U00096 CDS 283201- 285168

+ yagF b0269 JW0262 EcoGene:EG13345 Phage or Prophage Related putative dehydratase 1 11 CP4-6 prophage;

dehydratase family protein AAC73372.1

RESULTS_dnaQ

RESULTS_CIQ2J 149.0 . 45 1.093621e+00 0.5 1 15,17,9,3 60 152 0.17,1,1,0.4 7.762504e-02 GT:PL:GQ 0/1:179,0,255:99

9 ^CHROM ^POS ^{ID REF ALT}

U00096 294225 . T G

G missense_variant MODERATE yagM b0279 transcript AAC73382.1 Coding 1/1 c.575A>C p.Asn192Thr 575/855 575/855 192/284 U00096 gene 293945-

294799

- yagM b0279 JW0273 EcoGene:EG13552

U00096 CDS 293945- 294799

- yagM b0279 JW0273 EcoGene:EG13552 Phage or Prophage Related 1 11 CP4-6 prophage; uncharacterized protein AAC73382.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 17 5.270463e-02 0.5 1 2,3,7,5 60 92 0.62,0.27,1,0.42 1.424752e-01 GT:PL:GQ 0/1:255,0,119:99

10 ^CHROM ^POS ^{ID REF ALT}

U00096 347903 . TGG TG

frameshift_variant HIGH prpR b0330 transcript AAC73433.1 Coding 1/1 c.539delC p.Ala180fs 539/1587 539/1587 180/528 U00096 gene 346857-

348443

- prpR b0330 yahP EcoGene:EG13600

(3)

U00096 CDS 346857- 348443

- prpR b0330 yahP EcoGene:EG13600 regulator; Not classified regulator for prp operon; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016564 - transcription repressor activity; GO_process: GO:0019395 - fatty acid oxidation;

GO_process: GO:0006350 - transcription 1 11 propionate catabolism operon regulatory protein AAC73433.1

RESULTS_dnaQ

RESULTS_CIQ2J 217.0 . 41 0.5 1 8,7,10,12 60 217 0.74,0.0097,1,0.052 2.831947e-01 17,0.414634 GT:PL:GQ 0/1:255,0,255:99

11 ^CHROM ^POS ^{ID REF ALT}

U00096 353323 . C G

G missense_variant MODERATE prpE b0335 transcript AAC73438.1 Coding 1/1 c.618C>G p.Ser206Arg 618/1887 618/1887 206/628 U00096 gene 352706-

354592

+ prpE b0335 yahU EcoGene:EG13604

U00096 CDS 352706- 354592

+ prpE b0335 yahU EcoGene:EG13604 putative enzyme; Not classified putative propionyl-CoA synthetase; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0019395 - fatty acid oxidation 1 11 propionate--CoA ligase AAC73438.1

RESULTS_dnaQ

12 ^CHROM ^POS ^{ID REF ALT}

U00096 396645 . A T

T stop_gained HIGH sbmA b0377 transcript AAC73480.1 Coding 1/1 c.7A>T p.Lys3* 7/1221 7/1221 3/406

U00096 gene 396639- 397859

+ sbmA b0377 JW0368 EcoGene:EG10928

U00096 CDS 396639- 397859

+ sbmA b0377 JW0368 EcoGene:EG10928 putative membrane; Drug/analog sensitivity sensitivity to microcin B17, possibly envelop protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0042493 - response to drug 1 11 peptide antibiotic transporter AAC73480.1

RESULTS_dnaQ

13 ^CHROM ^POS ^{ID REF ALT}

U00096 449803 . C A

A missense_variant MODERATE cyoB b0431 transcript AAC73534.1 Coding 1/1 c.839G>T p.Trp280Leu 839/1992 839/1992 280/663 U00096 gene 448650-

450641

- cyoB b0431 JW0421 EcoGene:EG10179

U00096 CDS 448650- 450641

- cyoB b0431 JW0421 EcoGene:EG10179 enzyme; Energy metabolism, carbon: Aerobic respiration GO_component:

GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process:

GO:0009060 - aerobic respiration 1 11 cytochrome o ubiquinol oxidase subunit I AAC73534.1 1.10.3.-

RESULTS_dnaQ

14 ^CHROM ^POS ^{ID REF ALT}

U00096 455934 . G A

A missense_variant MODERATE tig b0436 transcript AAC73539.1 Coding 1/1 c.802G>A p.Ala268Thr 802/1299 802/1299 268/432 U00096 gene 455133-

456431

+ tig b0436 JW0426 EcoGene:EG11003

U00096 CDS 455133- 456431

+ tig b0436 JW0426 EcoGene:EG11003 factor; Cell division trigger factor; a molecular chaperone involved in cell division;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006457 - protein folding 1 11 peptidyl-prolyl cis/trans isomerase (trigger factor) AAC73539.1 N-terminus verified by Edman degradation: PMID

2211496,2843289,9298646,9600841,9868784

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 31 1.901522e+00 0.5 1 9,4,8,10 60 199 0.27,1,1,1 1.238679e-01 GT:PL:GQ 0/1:255,0,226:99

15 ^CHROM ^POS ^{ID REF ALT}

U00096 461034 . T G

G missense_variant MODERATE lon b0439 transcript AAC73542.1 Coding 1/1 c.2147T>G p.Ile716Ser 2147/2355 2147/2355 716/784

(4)

U00096 gene 458888- 461242

+ lon b0439 muc EcoGene:EG10542

U00096 CDS 458888- 461242

+ lon b0439 muc EcoGene:EG10542 enzyme; Global regulatory functions DNA-binding, ATP-dependent protease La; heat shock K-protein; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0008233 - peptidase activity 1 11 DNA- binding ATP-dependent protease La AAC73542.1 3.4.21.53 N-terminus verified by Edman degradation: PMID 2984174,8294008

RESULTS_dnaQ

16 ^CHROM ^POS ^{ID REF ALT}

U00096 593174 . T C

C missense_variant MODERATE nfrB b0569 transcript AAC73670.1 Coding 1/1 c.5A>G p.Asp2Gly 5/2238 5/2238 2/745

C downstream_gene_variant MODIFIER cusS b0570 transcript AAC73671.1 Coding c.*1443A>G 154

U00096 gene 590941- 593178

- nfrB b0569 JW0558 EcoGene:EG11739

U00096 CDS 590941- 593178

- nfrB b0569 JW0558 EcoGene:EG11739 membrane; Phage-related functions and prophages bacteriophage N4 receptor, subunit, inner membrane protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 bacteriophage N4 receptor, inner membrane subunit AAC73670.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 17 1.212206e+00 0.5 1 3,2,6,6 60 91 1,1,1,1 8.387204e-02 GT:PL:GQ 0/1:255,0,118:99

17 ^CHROM ^POS ^{ID REF ALT}

U00096 656725 . T A

A missense_variant MODERATE pagP b0622 transcript AAC73723.1 Coding 1/1 c.169T>A p.Trp57Arg 169/561 169/561 57/186 U00096 gene 656557-

657117

+ pagP b0622 ybeG EcoGene:EG12180

U00096 CDS 656557- 657117

+ pagP b0622 ybeG EcoGene:EG12180 enzyme; Surface polysaccharides & antigens 1 11 phospholipid:lipid A palmitoyltransferase AAC73723.1 2.3.1.-

RESULTS_dnaQ

18 ^CHROM ^POS ^{ID REF ALT}

U00096 672149 . A T

T missense_variant MODERATE lptE b0641 transcript AAC73742.1 Coding 1/1 c.38T>A p.Val13Glu 38/582 38/582 13/193

T downstream_gene_variant MODIFIER leuS b0642 transcript AAC73743.1 Coding c.*2583T>A 52

U00096 gene 671605- 672186

- lptE b0641 rlpB EcoGene:EG10855

U00096 CDS 671605- 672186

- lptE b0641 rlpB EcoGene:EG10855 membrane; Macromolecule synthesis, modification: Lipoprotein a minor lipoprotein;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0042158 - lipoprotein biosynthetic process 1 11 LPS assembly OM complex LptDE, lipoprotein component AAC73742.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 28 -1.198658e-01 0.5 1 7,3,9,9 59 163 0.43,0.19,1,0.024 1.797401e-01 GT:PL:GQ 0/1:255,0,190:99

19 ^CHROM ^POS ^{ID REF ALT}

U00096 749412 . C G

G missense_variant MODERATE ybgP b0717 transcript AAC73811.1 Coding 1/1 c.296G>C p.Gly99Ala 296/729 296/729 99/242 U00096 gene 748979-

749707

- ybgP b0717 JW0707 EcoGene:EG13312

U00096 CDS 748979- 749707

- ybgP b0717 JW0707 EcoGene:EG13312 putative factor; Surface structures putative chaperone; GO_process:

GO:0006457 - protein folding 1 11 putative periplasmic pilin chaperone AAC73811.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 28 -1.323079e+00 0.5 1 7,5,7,9 59 210 0.7,0.4,0.2,1 1.651488e-01 GT:PL:GQ 0/1:255,0,237:99

20 ^CHROM ^POS ^{ID REF ALT}

(5)

U00096 814742 . G C

C missense_variant MODERATE uvrB b0779 transcript AAC73866.1 Coding 1/1 c.1217G>C p.Gly406Ala 1217/2022 1217/2022 406/673 U00096 gene 813526-

815547

+ uvrB b0779 JW0762 EcoGene:EG11062

U00096 CDS 813526- 815547

+ uvrB b0779 JW0762 EcoGene:EG11062 enzyme; Degradation of DNA DNA repair; excision nuclease subunit B;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006308 - DNA catabolic process; GO_process:

GO:0006281 - DNA repair; GO_process: GO:0009314 - response to radiation; GO_process: GO:0009432 - SOS response 1 11 exision nuclease of nucleotide excision repair, DNA damage recognition component AAC73866.1

RESULTS_dnaQ

21 ^CHROM ^POS ^{ID REF ALT}

U00096 871139 . A G

G missense_variant MODERATE gsiC b0831 transcript AAC73918.1 Coding 1/1 c.173A>G p.Asp58Gly 173/921 173/921 58/306

G downstream_gene_variant MODIFIER gsiB b0830 transcript AAC73917.1 Coding c.*1539A>G 190

U00096 gene 870967- 871887

+ gsiC b0831 yliC EcoGene:EG13474

U00096 CDS 870967- 871887

+ gsiC b0831 yliC EcoGene:EG13474 putative transport; Not classified putative transport system permease protein;

GO_component: GO:0019866 - organelle inner membrane 1 11 glutathione ABC transporter permease AAC73918.1

RESULTS_dnaQ

RESULTS_CIQ2J 3.54 . 26 1.605145e-01 0.4998 1 8,15,2,1 60 5.47 0.54,1,1,1 6.186179e-02 GT:PL:GQ 0/1:31,0,255:30

22 ^CHROM ^POS ^{ID REF ALT}

U00096 909605 . A T

T missense_variant MODERATE poxB b0871 transcript AAC73958.1 Coding 1/1 c.1445T>A p.Leu482Gln 1445/1719 1445/1719 482/572 U00096 gene 909331-

911049

- poxB b0871 JW0855 EcoGene:EG10754

U00096 CDS 909331- 911049

- poxB b0871 JW0855 EcoGene:EG10754 enzyme; Degradation of small molecules: Carbon compounds pyruvate oxidase;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process; GO_process:

GO:0042867 - pyruvate catabolic process 1 11 pyruvate dehydrogenase, thiamine triphosphate-binding, FAD-binding AAC73958.1 1.2.5.1 N-terminus verified by Edman degradation: PMID 3902830

RESULTS_dnaQ

23 ^CHROM ^POS ^{ID REF ALT}

U00096 933585 . C A

A missense_variant MODERATE ftsK b0890 transcript AAC73976.1 Coding 1/1 c.362C>A p.Ala121Glu 362/3990 362/3990 121/1329 U00096 gene 933224-

937213

+ ftsK b0890 JW0873 EcoGene:EG13226

U00096 CDS 933224- 937213

+ ftsK b0890 JW0873 EcoGene:EG13226 phenotype; Cell division cell division protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009432 - SOS response 1 11 DNA translocase at septal ring sorting daughter chromsomes AAC73976.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 32 -8.051091e-01 0.5 1 5,4,16,6 60 145 0.42,1,1,1 1.389109e-01 GT:PL:GQ 0/1:255,0,172:99

24 ^CHROM ^POS ^{ID REF ALT}

U00096 996703 . C G

G missense_variant MODERATE ssuA b0936 transcript AAC74022.2 Coding 1/1 c.242G>C p.Gly81Ala 242/960 242/960 81/319 U00096 gene 995985-

996944

- ssuA b0936 ycbO EcoGene:EG13707

U00096 CDS 995985- 996944

- ssuA b0936 ycbO EcoGene:EG13707 periplasmic-binding component of ABC superfamily; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006793 - phosphorus metabolic process 1 11 aliphatic sulfonate ABC transporter periplasmic binding protein AAC74022.2

RESULTS_dnaQ

(6)

25 ^CHROM ^POS ^{ID REF ALT}

U00096 1026163 . A C

C missense_variant MODERATE helD b0962 transcript AAC74048.1 Coding 1/1 c.1693A>C p.Ile565Leu 1693/2055 1693/2055 565/684 U00096 gene 1024471-

1026525

+ helD b0962 srjB EcoGene:EG10426

U00096 CDS 1024471- 1026525

+ helD b0962 srjB EcoGene:EG10426 enzyme; DNA - replication, repair, restriction/modification GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication 1 11 DNA helicase IV AAC74048.1 3.6.1.- N-terminus verified by Edman degradation: PMID 2542273

RESULTS_dnaQ

26 ^CHROM ^POS ^{ID REF ALT}

U00096 1042554 . C G

G missense_variant MODERATE etk b0981 transcript AAC74066.1 Coding 1/1 c.1657G>C p.Ala553Pro 1657/2181 1657/2181 553/726 U00096 gene 1042030-

1044210

- etk b0981 yccC EcoGene:EG11826

U00096 CDS 1042030- 1044210

- etk b0981 yccC EcoGene:EG11826 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0006464 - protein modification process 1 11 tyrosine-protein kinase, role in O-antigen capsule formation AAC74066.1 2.7.10.2 N-terminus verified by Edman degradation: PMID 10369665

RESULTS_dnaQ

27 ^CHROM ^POS ^{ID REF ALT}

U00096 1143915 . T A

A missense_variant MODERATE rne b1084 transcript AAC74168.1 Coding 1/1 c.453A>T p.Leu151Phe 453/3186 453/3186 151/1061 U00096 gene 1141182-

1144367

- rne b1084 smbB EcoGene:EG10859

U00096 CDS 1141182- 1144367

- rne b1084 smbB EcoGene:EG10859 enzyme; Degradation of RNA RNase E, membrane attachment, mRNA turnover, maturation 5S RNA; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006401 - RNA catabolic process 1 11 endoribonuclease; RNA-binding protein;RNA degradosome binding protein AAC74168.1 3.1.4.- N-terminus verified by Edman degradation: PMID 2011493

RESULTS_dnaQ

28 ^CHROM ^POS ^{ID REF ALT}

U00096 1163417 . A T

T missense_variant MODERATE thiK b1106 transcript AAC74190.1 Coding 1/1 c.158A>T p.Asp53Val 158/825 158/825 53/274

T downstream_gene_variant MODIFIER lpoB b1105 transcript AAC74189.1 Coding c.*642A>T 138

U00096 gene 1163260- 1164084

+ thiK b1106 ycfN EcoGene:EG13432

U00096 CDS 1163260- 1164084

+ thiK b1106 ycfN EcoGene:EG13432 enzyme; Biosynthesis of cofactors, carriers: Thiamine putative beta-glucosidase 1 11 thiamine kinase AAC74190.1 2.7.1.89

RESULTS_dnaQ

29 ^CHROM ^POS ^{ID REF ALT}

U00096 1182052 . C G

G missense_variant MODERATE potD b1123 transcript AAC74207.1 Coding 1/1 c.778G>C p.Ala260Pro 778/1047 778/1047 260/348 U00096 gene 1181783-

1182829

- potD b1123 JW1109 EcoGene:EG10752

U00096 CDS 1181783- 1182829

- potD b1123 JW1109 EcoGene:EG10752 transport; Transport of small molecules: Amino acids, amines

spermidine/putrescine periplasmic transport protein; periplasmic-binding component of ABC superfamily; GO_component:

GO:0042597 - periplasmic space; GO_process: GO:0006596 - polyamine biosynthetic process; GO_process:

(7)

GO:0009310 - amine catabolic process 1 11 spermidine/putrescine ABC transporter periplasmic binding protein AAC74207.1

RESULTS_dnaQ

30 ^CHROM ^POS ^{ID REF ALT}

U00096 1195945 . A C

C missense_variant MODERATE icd b1136 transcript AAC74220.1 Coding 1/1 c.823A>C p.Ile275Leu 823/1251 823/1251 275/416 U00096 gene 1195123-

1196373

+ icd b1136 JW1122 EcoGene:EG10489

U00096 CDS 1195123- 1196373

+ icd b1136 JW1122 EcoGene:EG10489 enzyme; Energy metabolism, carbon: TCA cycle; Phage or Prophage Related isocitrate dehydrogenase, specific for NADP+; GO_process: GO:0006099 - tricarboxylic acid cycle; GO_process:

GO:0009061 - anaerobic respiration 1 11 isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase AAC74220.1 1.1.1.42 N-terminus verified by Edman degradation: PMID 9298646

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 33 -9.903538e-01 0.5 1 6,3,13,11 59 138 0.7,0.29,0.27,1 1.678538e-01 GT:PL:GQ 0/1:255,0,165:99

31 ^CHROM ^POS ^{ID REF ALT}

U00096 1207789 . C G

G missense_variant MODERATE stfP b1154 transcript AAC74238.1 Coding 1/1 c.289C>G p.Leu97Val 289/630 289/630 97/209 U00096 gene 1207501-

1208130

+ stfP b1154 ycfK EcoGene:EG12877

U00096 CDS 1207501- 1208130

+ stfP b1154 ycfK EcoGene:EG12877 Phage or Prophage Related 1 11 e14 prophage; uncharacterized protein AAC74238.1

RESULTS_dnaQ

RESULTS_CIQ2J 45.0 . 17 -2.462343e+00 0.5 1 1,10,6,0 43 48 0.00057,1,0.012,1 1.427571e-02 GT:PL:GQ 0/1:75,0,171:78

32 ^CHROM ^POS ^{ID REF ALT}

U00096 1209619 . C G

G missense_variant MODERATE stfE b1157 transcript b1157 Coding 1/1 c.1G>C p.Val1Leu 1/501 1/501 1/166 WARNING_TRANSCRIPT_NO_START_CODON G upstream_gene_variant MODIFIER pinE b1158 transcript AAC74242.1 Coding c.-1C>G 66

U00096 gene 1209119- 1209619

- stfE b1157 ycfE EcoGene:EG11818

U00096 CDS 1209119- 1209619

- stfE b1157 ycfE EcoGene:EG11818 pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related 1 11

SAMPLE QUAL FILTER DP RPB AF1 AC1 DP4 MQ FQ PV4 VDB IS FORMAT VALUES

RESULTS_dnaQ

RESULTS_CIQ2J 53.0 . 21 3.618328e+00 0.5 1 12,2,0,7 43 56 0.00031,0.081,0.062,0.14 1.012038e-02 GT:PL:GQ 0/1:83,0,204:86

33 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1250829 . ATTTTTT ATTTTT

frameshift_variant HIGH dhaK b1200 transcript AAC74284.2 Coding 1/1 c.4delA p.Lys2fs 4/1071 4/1071 2/356 U00096 gene 1249768-

1250838

- dhaK b1200 ycgT EcoGene:EG13901

U00096 CDS 1249768- 1250838

- dhaK b1200 ycgT EcoGene:EG13901 putative enzyme; Not classified 1 11 dihydroxyacetone kinase, PTS-dependent, dihydroxyacetone-binding subunit AAC74284.2

RESULTS_dnaQ

RESULTS_CIQ2J 54.5 . 21 0.5 1 5,3,7,6 60 16.6 1,9e-06,1,1 1.936822e-01 13,0.619048 GT:PL:GQ 0/1:92,0,51:54

34 ^CHROM ^POS ^{ID REF ALT}

U00096 1281926 . T A

A missense_variant MODERATE narG b1224 transcript AAC74308.1 Coding 1/1 c.2063T>A p.Leu688Gln 2063/3744 2063/3744 688/1247 U00096 gene 1279864- + narG b1224 narC EcoGene:EG10638

(8)

1283607 U00096 CDS 1279864-

1283607

+ narG b1224 narC EcoGene:EG10638 enzyme; Energy metabolism, carbon: Anaerobic respiration GO_component:

GO:0009061 - anaerobic respiration 1 11 nitrate reductase 1, alpha subunit AAC74308.1 1.7.99.4

RESULTS_dnaQ

35 ^CHROM ^POS ^{ID REF ALT}

U00096 1296380 . T C

C missense_variant MODERATE adhE b1241 transcript AAC74323.1 Coding 1/1 c.1742A>G p.Tyr581Cys 1742/2676 1742/2676 581/891 U00096 gene 1295446-

1298121

- adhE b1241 JW1228 EcoGene:EG10031

U00096 CDS 1295446- 1298121

- adhE b1241 JW1228 EcoGene:EG10031 enzyme; Energy metabolism, carbon: Fermentation CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase; GO_process:

GO:0006113 - fermentation 1 11 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase AAC74323.1 1.2.1.10

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 27 2.714051e-01 0.5 1 2,9,9,7 60 170 0.11,1,1,0.028 1.418661e-01 GT:PL:GQ 0/1:255,0,197:99

36 ^CHROM ^POS ^{ID REF ALT}

U00096 1307693 . G A

A missense_variant MODERATE clsA b1249 transcript AAC74331.1 Coding 1/1 c.953C>T p.Pro318Leu 953/1461 953/1461 318/486 U00096 gene 1307185-

1308645

- clsA b1249 yciJ EcoGene:EG11608

U00096 CDS 1307185- 1308645

- clsA b1249 yciJ EcoGene:EG11608 enzyme; Macromolecule synthesis: Phospholipids cardiolipin synthase, a major membrane phospholipid; novobiocin sensitivity; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0008654 - phospholipid biosynthetic process; GO_process: GO:0042493 - response to drug 1 11 cardiolipin synthase 1 AAC74331.1 2.7.8.-

RESULTS_dnaQ

37 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1312205 . TAAAA TAAA

frameshift_variant HIGH yciA b1253 transcript AAC74335.1 Coding 1/1 c.38delT p.Val13fs 38/399 38/399 13/132

downstream_gene_variant MODIFIER yciB b1254 transcript AAC74336.1 Coding c.*540delT 142

U00096 gene 1311848-1312246 - yciA b1253 JW1245 EcoGene:EG11121

U00096 CDS 1311848-1312246 - yciA b1253 JW1245 EcoGene:EG11121 1 11 acyl-CoA esterase AAC74335.1

RESULTS_dnaQ

RESULTS_CIQ2J 156.0 . 31 0.5 1 4,4,9,13 59 44.5 0.7,3.3e-06,1,1 2.867594e-02 22,0.709677 GT:PL:GQ 0/1:194,0,79:82

38 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1328067 . GTTTT GTTT

frameshift_variant HIGH btuR b1270 transcript AAC74352.1 Coding 1/1 c.287delA p.Gln96fs 287/591 287/591 96/196 U00096 gene 1327767-

1328357

- btuR b1270 JW1262 EcoGene:EG10130

U00096 CDS 1327767- 1328357

- btuR b1270 JW1262 EcoGene:EG10130 enzyme; Biosynthesis of cofactors, carriers: Cobalamin cob(I)alamin adenolsyltransferase; GO_component: GO:0005737 - cytoplasm 1 11 cob(I)yrinic acid a,c-diamide adenosyltransferase AAC74352.1 2.5.1.17

RESULTS_dnaQ

RESULTS_CIQ2J 121.0 . 28 0.5 1 3,9,5,10 60 94.5 0.7,1.4e-06,1,1 1.918884e-01 15,0.535714 GT:PL:GQ 0/1:159,0,129:99

39 ^CHROM ^POS ^{ID REF ALT}

U00096 1349230 . T G

(9)

G missense_variant MODERATE yciW b1287 transcript AAC74369.2 Coding 1/1 c.878A>C p.Lys293Thr 878/1128 878/1128 293/375 U00096 gene 1348980-

1350107

- yciW b1287 JW5200 EcoGene:EG14262

U00096 CDS 1348980- 1350107

- yciW b1287 JW5200 EcoGene:EG14262 putative enzyme; Not classified 1 11 putative oxidoreductase AAC74369.2

RESULTS_dnaQ

RESULTS_CIQ2J 199.0 . 15 -7.938566e-01 0.5 1 2,1,9,3 60 35 1,0.33,1,0.086 1.208052e-01 GT:PL:GQ 0/1:229,0,62:65

40 ^CHROM ^POS ^{ID REF ALT}

U00096 1376140 . T G

G missense_variant MODERATE ycjR b1314 transcript AAC74396.2 Coding 1/1 c.107T>G p.Leu36Arg 107/789 107/789 36/262

G downstream_gene_variant MODIFIER ycjQ b1313 transcript AAC74395.1 Coding c.*1053T>G 125

U00096 gene 1376034- 1376822

+ ycjR b1314 JW5202 EcoGene:EG13915

U00096 CDS 1376034- 1376822

+ ycjR b1314 JW5202 EcoGene:EG13915 putative factor; Not classified 1 11 putative TIM alpha/beta barrel enzyme AAC74396.2

RESULTS_dnaQ

RESULTS_CIQ2J 216.0 . 26 1.361111e+00 0.5 1 7,1,15,3 60 111 1,0.43,1,0.1 1.853846e-01 GT:PL:GQ 0/1:246,0,138:99

41 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1412991 . GTTTTT GTTTT

frameshift_variant HIGH intR b1345 transcript AAC74427.1 Coding 1/1 c.240delA p.Ile80fs 240/1236 240/1236 80/411

U00096 gene 1412000-1413235 - intR b1345 ydaP EcoGene:EG13358

U00096 CDS 1412000-1413235 - intR b1345 ydaP EcoGene:EG13358 Phage or Prophage Related 1 11 Rac prophage; integrase AAC74427.1

RESULTS_dnaQ

RESULTS_CIQ2J 65.5 . 16 0.5 1 2,4,5,5 60 22.5 0.63,0.0032,1,1 9.285752e-02 10,0.625000 GT:PL:GQ 0/1:103,0,57:60

42 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1442097 . ATTTTT ATTTT

frameshift_variant HIGH ldhA b1380 transcript AAC74462.1 Coding 1/1 c.742delA p.Lys248fs 742/990 742/990 248/329 U00096 gene 1441854-

1442843

- ldhA b1380 JW1375 EcoGene:EG13186

U00096 CDS 1441854- 1442843

- ldhA b1380 JW1375 EcoGene:EG13186 enzyme; Energy metabolism, carbon: Fermentation GO_process: GO:0006113 - fermentation 1 11 fermentative D-lactate dehydrogenase, NAD-dependent AAC74462.1 1.1.1.28

RESULTS_dnaQ

RESULTS_CIQ2J 136.0 . 19 1 2 0,0,10,8 60 -88.5 1.303258e-01 18,0.947368 GT:PL:GQ 1/1:177,54,0:99

43 ^CHROM ^POS ^{ID REF ALT}

U00096 1442546 . A C

C missense_variant MODERATE ldhA b1380 transcript AAC74462.1 Coding 1/1 c.298T>G p.Tyr100Asp 298/990 298/990 100/329 U00096 gene 1441854-

1442843

- ldhA b1380 JW1375 EcoGene:EG13186

U00096 CDS 1441854- 1442843

- ldhA b1380 JW1375 EcoGene:EG13186 enzyme; Energy metabolism, carbon: Fermentation GO_process: GO:0006113 - fermentation 1 11 fermentative D-lactate dehydrogenase, NAD-dependent AAC74462.1 1.1.1.28

RESULTS_dnaQ

44 ^CHROM ^POS ^{ID REF ALT}

U00096 1472567 . C G

G missense_variant MODERATE ydbA b4492 transcript b4492 Coding 3/3 c.4617C>G p.Ser1539Arg 4617/6063 4617/6063 1539/2020 U00096 gene 1465392-1467904,1469241- + ydbA b4492 JW5802 EcoGene:EG11307

(10)

1469293,1470517-1474013 U00096 CDS 1465392-1467904,1469241-

1469293,1470517-1474013

+ ydbA b4492 JW5802 EcoGene:EG11307 pseudogene, autotransporter homolog;

interrupted by IS2 and IS30 1 11

RESULTS_dnaQ

RESULTS_CIQ2J 222.0 . 36 8.663597e-01 1 2 1,0,18,17 60 -97 1,0.38,1,1 2.272670e-01 GT:PL:GQ 1/1:255,70,0:99

45 ^CHROM ^POS ^{ID REF ALT}

U00096 1506320 . C A

A missense_variant MODERATE ydcN b1434 transcript AAC74516.1 Coding 1/1 c.149C>A p.Ala50Glu 149/537 149/537 50/178 U00096 gene 1506172-

1506708

+ ydcN b1434 JW1430 EcoGene:EG13757

U00096 CDS 1506172- 1506708

+ ydcN b1434 JW1430 EcoGene:EG13757 putative regulator; Not classified 1 11 putative DNA-binding transcriptional regulator AAC74516.1

RESULTS_dnaQ

46 ^CHROM ^POS ^{ID REF ALT}

U00096 1529128 . GC GCC

C frameshift_variant HIGH rhsE b1456 transcript b1456 Coding 1/1 c.1228dupC p.Gln410fs 1229/2037 1229/2037 410/678 WARNING_TRANSCRIPT_NO_START_CODON

U00096 gene 1527902-1529938 + rhsE b1456 JW1451 EcoGene:EG10010

U00096 CDS 1527902-1529938 + rhsE b1456 JW1451 EcoGene:EG10010 pseudogene, Rhs family 1 11

RESULTS_dnaQ

RESULTS_CIQ2J 125.0 . 31 0.5 1 5,14,5,7 34 128 0.45,1,1,1 2.572837e-01 11,0.354839 GT:PL:GQ 0/1:163,0,191:99

47 ^CHROM ^POS ^{ID REF ALT}

U00096 1562457 . G A

A missense_variant MODERATE ddpA b1487 transcript AAC74560.1 Coding 1/1 c.25C>T p.Pro9Ser 25/1551 25/1551 9/516

A downstream_gene_variant MODIFIER ddpX b1488 transcript AAC74561.1 Coding c.*582C>T 38

U00096 gene 1560931- 1562481

- ddpA b1487 yddS EcoGene:EG13790

U00096 CDS 1560931- 1562481

- ddpA b1487 yddS EcoGene:EG13790 putative factor; Not classified periplasmic-binding component of ABC superfamily;

GO_component: GO:0042597 - periplasmic space 1 11 D,D-dipeptide ABC transporter periplasmic binding protein AAC74560.1

RESULTS_dnaQ

48 ^CHROM ^POS ^{ID REF ALT}

U00096 1572565 . T C

C missense_variant MODERATE pqqL b1494 transcript AAC74567.1 Coding 1/1 c.2638A>G p.Thr880Ala 2638/2796 2638/2796 880/931 U00096 gene 1572407-

1575202

- pqqL b1494 yddC EcoGene:EG11744

U00096 CDS 1572407- 1575202

- pqqL b1494 yddC EcoGene:EG11744 putative enzyme; Not classified putative zinc protease; GO_component:

GO:0005737 - cytoplasm 1 11 putative periplasmic M16 family zinc metalloendopeptidase AAC74567.1

RESULTS_dnaQ

49 ^CHROM ^POS ^{ID REF ALT}

U00096 1650406 . C T

T missense_variant MODERATE ydfE b1577 transcript b1577 Coding 1/1 c.329C>T p.Ala110Val 329/765 329/765 110/254 WARNING_TRANSCRIPT_NO_STOP_CODON T intron_variant MODIFIER ydfJ b4600 transcript b4600 Coding 1/1 c.84+2349G>A

U00096 gene 1650078-1650842 + ydfE b1577 JW1568 EcoGene:EG11304

U00096 CDS 1650078-1650842 + ydfE b1577 JW1568 EcoGene:EG11304 Qin prophage; pseudogene;Phage or Prophage Related 1 11

(11)

SAMPLE QUAL FILTER DP RPB AF1 AC1 DP4 MQ FQ PV4 VDB IS FORMAT VALUES RESULTS_dnaQ

50 ^CHROM ^POS ^{ID REF ALT}

U00096 1652922 . T A

A stop_gained HIGH rspB b1580 transcript AAC74652.1 Coding 1/1 c.994A>T p.Lys332* 994/1020 994/1020 332/339

A upstream_gene_variant MODIFIER ydfJ b4600 transcript b4600 Coding c.-1A>T 84

U00096 gene 1652896- 1653915

- rspB b1580 JW1572 EcoGene:EG12452

U00096 CDS 1652896- 1653915

- rspB b1580 JW1572 EcoGene:EG12452 enzyme; Global regulatory functions starvation sensing protein; GO_process:

GO:0042594 - response to starvation 1 11 putative Zn-dependent NAD(P)-binding oxidoreductase AAC74652.1

RESULTS_dnaQ

RESULTS_CIQ2J 148.0 . 13 -9.716262e-01 0.5 1 3,3,4,3 60 130 1,0.19,1,1 8.329641e-02 GT:PL:GQ 0/1:178,0,157:99

51 ^CHROM ^POS ^{ID REF} ^ALT

U00096 1661238 . GAAA GAA

frameshift_variant HIGH ynfF b1588 transcript AAC74660.4 Coding 1/1 c.686delA p.Asn229fs 686/2424 686/2424 229/807 U00096 gene 1660556-

1662979

+ ynfF b1588 JW5260 EcoGene:EG13844

U00096 CDS 1660556- 1662979

+ ynfF b1588 JW5260 EcoGene:EG13844 putative enzyme; Not classified 1 11 S- and N-oxide reductase, A subunit, periplasmic AAC74660.4

RESULTS_dnaQ

RESULTS_CIQ2J 131.0 . 20 0.5 1 4,4,3,6 60 127 0.64,1.7e-14,1,0.065 1.792966e-01 10,0.500000 GT:PL:GQ 0/1:169,0,162:99

52 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1693152 . CGGG CGG

frameshift_variant HIGH uidB b1616 transcript AAC74688.1 Coding 1/1 c.1109delC p.Thr370fs 1109/1374 1109/1374 370/457 U00096 gene 1692890-

1694263

- uidB b1616 uidP EcoGene:EG11658

U00096 CDS 1692890- 1694263

- uidB b1616 uidP EcoGene:EG11658 transport; Transport of small molecules: Carbohydrates, organic acids, alcohols glucuronide permease; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 glucuronide transporter AAC74688.1 N-terminus verified by Edman degradation: PMID 15774881

RESULTS_dnaQ

RESULTS_CIQ2J 192.0 . 24 0.5 1 2,4,12,5 60 58.5 0.16,1,1,1 1.285282e-01 15,0.625000 GT:PL:GQ 0/1:230,0,93:96

53 ^CHROM ^POS ^{ID REF ALT}

U00096 1807667 . GAA GA

frameshift_variant HIGH ydiZ b1724 transcript AAC74794.1 Coding 1/1 c.270delA p.Glu90fs 270/291 270/291 90/96

upstream_gene_variant MODIFIER yniA b1725 transcript AAC74795.1 Coding c.-1delA 127

U00096 gene 1807400-1807690 + ydiZ b1724 JW1713 EcoGene:EG13985

U00096 CDS 1807400-1807690 + ydiZ b1724 JW1713 EcoGene:EG13985 1 11 uncharacterized protein AAC74794.1

RESULTS_dnaQ

RESULTS_CIQ2J 153.0 . 16 0.5 1 4,3,4,5 60 148 1,5.4e-14,1,0.49 1.617725e-01 9,0.562500 GT:PL:GQ 0/1:191,0,183:99

54 ^CHROM ^POS ^{ID REF ALT}

U00096 1832908 . A G

G missense_variant MODERATE xthA b1749 transcript AAC74819.1 Coding 1/1 c.481A>G p.Ile161Val 481/807 481/807 161/268 U00096 gene 1832428-

1833234

+ xthA b1749 xth EcoGene:EG11073

U00096 CDS 1832428- 1833234

+ xthA b1749 xth EcoGene:EG11073 enzyme; Degradation of DNA GO_process: GO:0006308 - DNA catabolic process;

GO_process: GO:0009314 - response to radiation 1 11 exonuclease III AAC74819.1 3.1.11.2

(12)

SAMPLE QUAL FILTER DP RPB AF1 AC1 DP4 MQ FQ PV4 VDB IS FORMAT VALUES RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 28 1.411211e+00 0.5 1 9,2,8,9 59 160 0.11,0.23,1,0.24 1.661622e-01 GT:PL:GQ 0/1:255,0,187:99

55 ^CHROM ^POS ^{ID REF ALT}

U00096 1899060 . A C

C missense_variant MODERATE yoaD b1815 transcript AAC74885.2 Coding 1/1 c.634A>C p.Asn212His 634/1599 634/1599 212/532 U00096 gene 1898427-

1900025

+ yoaD b1815 JW1804 EcoGene:EG13516

U00096 CDS 1898427- 1900025

+ yoaD b1815 JW1804 EcoGene:EG13516 1 11 putative membrane-anchored cyclic-di-GMP phosphodiesterase, regulator of cellulose production AAC74885.2

RESULTS_dnaQ

56 ^CHROM ^POS ^{ID REF ALT}

U00096 1925214 . T G

G missense_variant MODERATE holE b1842 transcript AAC74912.1 Coding 1/1 c.107T>G p.Ile36Ser 107/231 107/231 36/76 U00096 gene 1925108-

1925338

+ holE b1842 JW1831 EcoGene:EG11505

U00096 CDS 1925108- 1925338

+ holE b1842 JW1831 EcoGene:EG11505 enzyme; DNA - replication, repair, restriction/modification GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication 1 11 DNA polymerase III, theta subunit AAC74912.1 2.7.7.7 N-terminus verified by Edman degradation: PMID 8246893,8505306

RESULTS_dnaQ

57 ^CHROM ^POS ^{ID REF ALT}

U00096 1967269 . C A

A missense_variant MODERATE cheY b1882 transcript AAC74952.1 Coding 1/1 c.169G>T p.Asp57Tyr 169/390 169/390 57/129

A downstream_gene_variant MODIFIER cheB b1883 transcript AAC74953.1 Coding c.*1050G>T 183

U00096 gene 1967048- 1967437

- cheY b1882 JW1871 EcoGene:EG10150

U00096 CDS 1967048- 1967437

- cheY b1882 JW1871 EcoGene:EG10150 regulator; Chemotaxis and mobility chemotaxis regulator transmits chemoreceptor signals to flagelllar motor components; GO_component: GO:0005737 - cytoplasm; GO_process:

GO:0042330 - taxis 1 11 chemotaxis regulator transmitting signal to flagellar motor component AAC74952.1

RESULTS_dnaQ

58 ^CHROM ^POS ^{ID REF ALT}

U00096 1971418 . C A

A missense_variant MODERATE tar b1886 transcript AAC74956.1 Coding 1/1 c.1274G>T p.Arg425Leu 1274/1662 1274/1662 425/553 U00096 gene 1971030-

1972691

- tar b1886 JW1875 EcoGene:EG10988

U00096 CDS 1971030- 1972691

- tar b1886 JW1875 EcoGene:EG10988 regulator; Chemotaxis and mobility methyl-accepting chemotaxis protein II, aspartate sensor receptor; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0042330 - taxis 1 11 methyl-accepting chemotaxis protein II AAC74956.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 24 -1.550340e+00 0.5 1 8,1,7,8 60 130 0.08,0.094,1,1 5.998678e-02 GT:PL:GQ 0/1:255,0,157:99

59 ^CHROM ^POS ^{ID REF ALT}

U00096 1977712 . T C

C missense_variant MODERATE flhC b1891 transcript AAC74961.1 Coding 1/1 c.133A>G p.Lys45Glu 133/579 133/579 45/192

C downstream_gene_variant MODIFIER flhD b1892 transcript AAC74962.2 Coding c.*351A>G 135

U00096 gene 1977266- - flhC b1891 JW1880 EcoGene:EG10319

(13)

1977844 U00096 CDS 1977266-

1977844

- flhC b1891 JW1880 EcoGene:EG10319 regulator; Surface structures regulator of flagellar biosynthesis acting on class 2 operons; transcription initiation factor?; GO_component: GO:0019861 - flagellum; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity; GO_process: GO:0009296 - flagellum assembly;

GO_process: GO:0006350 - transcription; GO_process: GO:0042330 - taxis 1 11 flagellar class II regulon transcriptional activator, with FlhD AAC74961.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 21 -9.547859e-01 0.5002 1 0,3,5,13 60 5.47 0.55,1,1,1 1.600538e-01 GT:PL:GQ 0/1:255,0,31:34

60 ^CHROM ^POS ^{ID REF ALT}

U00096 1990885 . T A

A missense_variant MODERATE tyrP b1907 transcript AAC74977.1 Coding 1/1 c.1205T>A p.Val402Glu 1205/1212 1205/1212 402/403

A downstream_gene_variant MODIFIER yecA b1908 transcript AAC74978.1 Coding c.*666A>T 69

U00096 gene 1989681- 1990892

+ tyrP b1907 JW1895 EcoGene:EG11041

U00096 CDS 1989681- 1990892

+ tyrP b1907 JW1895 EcoGene:EG11041 transport; Transport of small molecules: Amino acids, amines tyrosine-specific transport system; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006571 - tyrosine biosynthetic process 1 11 tyrosine transporter AAC74977.1

RESULTS_dnaQ

61 ^CHROM ^POS ^{ID REF ALT}

U00096 2014078 . G A

A missense_variant MODERATE fliF b1938 transcript AAC75005.1 Coding 1/1 c.850G>A p.Asp284Asn 850/1659 850/1659 284/552 U00096 gene 2013229-

2014887

+ fliF b1938 JW1922 EcoGene:EG11347

U00096 CDS 2013229- 2014887

+ fliF b1938 JW1922 EcoGene:EG11347 structural component; Surface structures flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein; GO_component: GO:0019861 - flagellum; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0009296 - flagellum assembly; GO_process: GO:0042330 - taxis 1 11 flagellar basal-body MS-ring and collar protein AAC75005.1

RESULTS_dnaQ

62 ^CHROM ^POS ^ID ^REF ^ALT

U00096 2037586 . CTTTTT CTTTTTT

T frameshift_variant HIGH yedV b1968 transcript AAC75034.1 Coding 1/1 c.561_562insA p.Lys188fs 561/1359 561/1359 187/452 U00096 gene 2036794-

2038152

- yedV b1968 JW1951 EcoGene:EG14044

U00096 CDS 2036794- 2038152

- yedV b1968 JW1951 EcoGene:EG14044 putative regulator; Not classified putative 2-component sensor protein;

GO_process: GO:0006464 - protein modification process 1 11 putative sensory kinase in two-component regulatory system with YedW AAC75034.1

RESULTS_dnaQ

RESULTS_CIQ2J 60.5 . 19 0.5003 1 1,3,2,9 58 -6.6 1,1,1,1 1.684552e-01 11,0.578947 GT:PL:GQ 0/1:98,0,29:32

63 ^CHROM ^POS ^{ID REF ALT}

U00096 2065074 . A G

G missense_variant MODERATE cobS b1992 transcript AAC75053.1 Coding 1/1 c.149T>C p.Leu50Pro 149/744 149/744 50/247

G downstream_gene_variant MODIFIER cobU b1993 transcript AAC75054.1 Coding c.*546T>C 145

U00096 gene 2064479- 2065222

- cobS b1992 JW1970 EcoGene:EG12150

U00096 CDS 2064479- 2065222

- cobS b1992 JW1970 EcoGene:EG12150 enzyme; Biosynthesis of cofactors, carriers: Cobalamin 1 11 cobalamin synthase AAC75053.1 2.-.-.-

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 20 1.584858e+00 0.5 1 4,3,5,8 60 134 0.64,0.21,1,0.13 1.507371e-01 GT:PL:GQ 0/1:255,0,161:99

(14)

64 ^CHROM ^POS ^{ID REF ALT}

U00096 2075218 . C A

A missense_variant MODERATE yeeR b2001 transcript AAC75062.2 Coding 1/1 c.440C>A p.Ala147Glu 440/1533 440/1533 147/510 U00096 gene 2074779-

2076311

+ yeeR b2001 JW1983 EcoGene:EG13385

U00096 CDS 2074779- 2076311

+ yeeR b2001 JW1983 EcoGene:EG13385 Phage or Prophage Related 1 11 CP4-44 prophage; putative membrane protein AAC75062.2

RESULTS_dnaQ

65 ^CHROM ^POS ^{ID REF ALT}

U00096 2107517 . A T

T missense_variant MODERATE glf b2036 transcript AAC75097.1 Coding 1/1 c.813T>A p.Asp271Glu 813/1104 813/1104 271/367 U00096 gene 2107226-

2108329

- glf b2036 yefE EcoGene:EG11981

U00096 CDS 2107226- 2108329

- glf b2036 yefE EcoGene:EG11981 enzyme; Degradation of small molecules: Carbon compounds UDP-galactopyranose mutase; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_function: GO:0042280 - cell surface antigen activity, host-interacting; GO_process: GO:0009243 - O antigen biosynthetic process 1 11 UDP-galactopyranose mutase, FAD/NAD(P)-binding AAC75097.1 5.4.99.9 N-terminus verified by Edman degradation: PMID 8576037

RESULTS_dnaQ

66 ^CHROM ^POS ^{ID REF ALT}

U00096 2140712 . C A

A stop_gained HIGH asmA b2064 transcript AAC75125.1 Coding 1/1 c.901G>T p.Glu301* 901/1854 901/1854 301/617 U00096 gene 2139759-

2141612

- asmA b2064 yegA EcoGene:EG11361

U00096 CDS 2139759- 2141612

- asmA b2064 yegA EcoGene:EG11361 phenotype; Outer membrane constituents suppressor of ompF assembly mutants;

GO_function: GO:0042280 - cell surface antigen activity, host-interacting; GO_process: GO:0009103 - lipopolysaccharide biosynthetic process 1 11 suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane-anchored periplasmic protein AAC75125.1

RESULTS_dnaQ

67 ^CHROM ^POS ^{ID REF ALT}

U00096 2183270 . C A

A missense_variant MODERATE yegX b2102 transcript AAC75163.2 Coding 1/1 c.382G>T p.Ala128Ser 382/819 382/819 128/272

U00096 gene 2182833-2183651 - yegX b2102 JW5345 EcoGene:EG14067

U00096 CDS 2182833-2183651 - yegX b2102 JW5345 EcoGene:EG14067 1 11 putative family 25 glycosyl hydrolase AAC75163.2

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 22 2.194274e+00 0.5 1 4,0,8,9 60 31 0.1,1,1,1 1.134917e-01 GT:PL:GQ 0/1:255,0,58:61

68 ^CHROM ^POS ^{ID REF ALT}

U00096 2233379 . GCC GC

frameshift_variant HIGH sanA b2144 transcript AAC75205.1 Coding 1/1 c.504delC p.Ala168fs 504/720 504/720 168/239 U00096 gene 2232878-

2233597

+ sanA b2144 yeiF EcoGene:EG12025

U00096 CDS 2232878- 2233597

+ sanA b2144 yeiF EcoGene:EG12025 transport; Drug/analog sensitivity vancomycin sensitivity; sanA mutant has a defective envelope more permeable to vancomycin at 42 degrees; GO_process: GO:0042493 - response to drug 1 11 DUF218 superfamily vancomycin high temperature exclusion protein AAC75205.1

RESULTS_dnaQ

RESULTS_CIQ2J 188.0 . 32 0.5 1 5,14,6,7 60 191 0.28,1,1,1 1.901357e-01 12,0.375000 GT:PL:GQ 0/1:226,0,255:99

(15)

69 ^CHROM ^POS ^{ID REF ALT}

U00096 2250252 . T C

C missense_variant MODERATE yeiH b2158 transcript AAC75219.1 Coding 1/1 c.536T>C p.Phe179Ser 536/1050 536/1050 179/349

U00096 gene 2249717-2250766 + yeiH b2158 JW2145 EcoGene:EG12027

U00096 CDS 2249717-2250766 + yeiH b2158 JW2145 EcoGene:EG12027 1 11 UPF0324 family inner membrane protein AAC75219.1

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 39 1.467677e+00 0.5 1 8,6,9,15 60 210 0.32,0.37,1,1 2.416177e-01 GT:PL:GQ 0/1:255,0,237:99

70 ^CHROM ^POS ^{ID REF ALT}

U00096 2275772 . A G

G missense_variant MODERATE yejE b2179 transcript AAC75240.1 Coding 1/1 c.500A>G p.Tyr167Cys 500/1026 500/1026 167/341 U00096 gene 2275273-

2276298

+ yejE b2179 JW2167 EcoGene:EG12040

U00096 CDS 2275273- 2276298

+ yejE b2179 JW2167 EcoGene:EG12040 putative transport; Not classified putative transport system permease protein;

membrane component of ABC superfamily; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane 1 11 microcin C ABC transporter permease AAC75240.1

RESULTS_dnaQ

71 ^CHROM ^POS ^{ID REF ALT}

U00096 2325411 . T A

A missense_variant MODERATE atoE b2223 transcript AAC75283.1 Coding 1/1 c.656T>A p.Leu219Gln 656/1323 656/1323 219/440 U00096 gene 2324756-

2326078

+ atoE b2223 JW2217 EcoGene:EG11671

U00096 CDS 2324756- 2326078

+ atoE b2223 JW2217 EcoGene:EG11671 transport; Degradation of small molecules: Fatty acids GO_component:

GO:0019395 - fatty acid oxidation 1 11 short chain fatty acid transporter AAC75283.1

RESULTS_dnaQ

RESULTS_CIQ2J 145.0 . 25 7.642870e-01 0.5 1 6,10,5,4 60 148 0.43,0.043,1,1 3.382970e-02 GT:PL:GQ 0/1:175,0,255:99

72 ^CHROM ^POS ^{ID REF ALT}

U00096 2327042 . G T

T missense_variant MODERATE atoB b2224 transcript AAC75284.1 Coding 1/1 c.934G>T p.Asp312Tyr 934/1185 934/1185 312/394 U00096 gene 2326109-

2327293

+ atoB b2224 JW2218 EcoGene:EG11672

U00096 CDS 2326109- 2327293

+ atoB b2224 JW2218 EcoGene:EG11672 enzyme; Degradation of small molecules: Fatty acids GO_process:

GO:0019395 - fatty acid oxidation 1 11 acetyl-CoA acetyltransferase AAC75284.1 2.3.1.9

RESULTS_dnaQ

RESULTS_CIQ2J 225.0 . 32 2.236068e-01 0.5 1 6,4,6,16 60 160 0.12,1,1,0.11 1.141773e-01 GT:PL:GQ 0/1:255,0,187:99

73 ^CHROM ^POS ^ID ^REF ^ALT

U00096 2396619 . GTTTT GTTT

frameshift_variant HIGH nuoH b2282 transcript AAC75342.1 Coding 1/1 c.820delA p.Lys274fs 820/978 820/978 274/325

upstream_gene_variant MODIFIER nuoI b2281 transcript AAC75341.1 Coding c.-1delA 173

U00096 gene 2396465- 2397442

- nuoH b2282 JW2277 EcoGene:EG12088

U00096 CDS 2396465- 2397442

- nuoH b2282 JW2277 EcoGene:EG12088 enzyme; Energy metabolism, carbon: Aerobic respiration NADH dehydrogenase I chain H; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009060 - aerobic respiration; GO_process: GO:0009061 - anaerobic respiration 1 11 NADH:ubiquinone oxidoreductase, membrane subunit H AAC75342.1

RESULTS_dnaQ

RESULTS_CIQ2J 121.0 . 27 0.5 1 7,4,8,6 60 92.5 1,5.9e-17,1,0.18 6.533553e-02 14,0.518519 GT:PL:GQ 0/1:159,0,127:99

(16)

74 ^CHROM ^POS ^{ID REF ALT}

U00096 2406429 . GCC GC

frameshift_variant HIGH lrhA b2289 transcript AAC75349.1 Coding 1/1 c.211delG p.Gly71fs 211/939 211/939 71/312 U00096 gene 2405703-

2406641

- lrhA b2289 JW2284 EcoGene:EG12123

U00096 CDS 2405703- 2406641

- lrhA b2289 JW2284 EcoGene:EG12123 regulator; Energy metabolism, carbon: Aerobic respiration GO_component:

GO:0005737 - cytoplasm; GO_function: GO:0016564 - transcription repressor activity; GO_process: GO:0009060 - aerobic respiration; GO_process: GO:0006350 - transcription 1 11 transcriptional repressor of flagellar, motility and chemotaxis genes AAC75349.1

RESULTS_dnaQ

RESULTS_CIQ2J 217.0 . 31 0.5 1 5,3,15,7 60 132 1,1,1,0.043 1.384221e-01 18,0.580645 GT:PL:GQ 0/1:255,0,167:99

75 ^CHROM ^POS ^{ID REF ALT}

U00096 2513154 . T C

C missense_variant MODERATE nupC b2393 transcript AAC75452.1 Coding 1/1 c.113T>C p.Val38Ala 113/1203 113/1203 38/400 U00096 gene 2513042-

2514244

+ nupC b2393 JW2389 EcoGene:EG11971

U00096 CDS 2513042- 2514244

+ nupC b2393 JW2389 EcoGene:EG11971 transport; Transport of small molecules: Nucleosides, purines, pyrimidines permease of transport system for 3 nucleosides; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 nucleoside (except guanosine) transporter AAC75452.1

RESULTS_dnaQ

76 ^CHROM ^POS ^{ID REF ALT}

U00096 2517363 . A G

G missense_variant MODERATE yfeA b2395 transcript AAC75454.2 Coding 1/1 c.470T>C p.Phe157Ser 470/2190 470/2190 157/729

U00096 gene 2515643-2517832 - yfeA b2395 JW5391 EcoGene:EG11145

U00096 CDS 2515643-2517832 - yfeA b2395 JW5391 EcoGene:EG11145 1 11 putative diguanylate cyclase AAC75454.2

RESULTS_dnaQ

RESULTS_CIQ2J 4.13 . 2 -9.668049e-01 0.5 1 1,0,0,1 60 4.13 1,1,1,1 GT:PL:GQ 0/1:32,0,32:31

77 ^CHROM ^POS ^{ID REF ALT}

U00096 2660768 . G C

C missense_variant MODERATE iscS b2530 transcript AAT48142.1 Coding 1/1 c.764C>G p.Ala255Gly 764/1215 764/1215 255/404 U00096 gene 2660317-

2661531

- iscS b2530 yzzO EcoGene:EG12677

U00096 CDS 2660317- 2661531

- iscS b2530 yzzO EcoGene:EG12677 enzyme; tRNA modification cysteine desulfurase; cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent; GO_process: GO:0009451 - RNA modification 1 11 cysteine desulfurase (tRNA sulfurtransferase), PLP-dependent AAT48142.1 2.8.1.7 N-terminus verified by Edman degradation: PMID 9298646

RESULTS_dnaQ

78 ^CHROM ^POS ^{ID REF ALT}

U00096 2692082 . C G

G missense_variant MODERATE purL b2557 transcript AAT48143.1 Coding 1/1 c.3462G>C p.Trp1154Cys 3462/3888 3462/3888 1154/1295 U00096 gene 2691656-

2695543

- purL b2557 purI EcoGene:EG10797

U00096 CDS 2691656- 2695543

- purL b2557 purI EcoGene:EG10797 enzyme; Purine ribonucleotide biosynthesis phosphoribosylformyl-glycineamide synthetase = FGAM synthetase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006164 - purine nucleotide biosynthetic process 1 11 phosphoribosylformyl-glycineamide synthetase AAT48143.1 6.3.5.3 N-terminus verified by Edman degradation: PMID 2659070

RESULTS_dnaQ

Non synonimous mutations found in sample: CIQ2J