Non synonimous mutations found in sample: CIQ1E

(1)

Non synonimous mutations found in sample: CIQ1E

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 11254 . CTTTTT CTTTT

frameshift_variant HIGH yaaW b0011 transcript AAC73122.1 Coding 1/1 c.98delA p.Glu33fs 98/714 98/714 33/237

downstream_gene_variant MODIFIER yaaI b0013 transcript AAC73124.1 Coding c.*405delA 123

U00096 gene 10643-11356 - yaaW b0011 JW0010 EcoGene:EG14340

U00096 CDS 10643-11356 - yaaW b0011 JW0010 EcoGene:EG14340 putative enzyme; Not classified 1 11 UPF0174 family protein AAC73122.1

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

RESULTS_dnaQ

RESULTS_CIQ1E 131.0 . 22 1 2 0,0,13,7 60 -94.5 1.956899e-01 19,0.863636 GT:PL:GQ 1/1:172,60,0:99

2 CHROM POS ID REF ALT U00096 19070 . T C

C missense_variant MODERATE nhaR b0020 transcript AAC73131.1 Coding 1/1 c.356T>C p.Val119Ala 356/906 356/906 119/301 U00096 gene 18715-

19620

+ nhaR b0020 yaaB EcoGene:EG11078

U00096 CDS 18715- 19620

+ nhaR b0020 yaaB EcoGene:EG11078 regulator; Transport of small molecules: Cations GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity; GO_process: GO:0006350 - transcription;

GO_process: GO:0009268 - response to pH 1 11 transcriptional activator of nhaA AAC73131.1

RESULTS_dnaQ

RESULTS_CIQ1E 222.0 . 41 1 2 0,0,18,23 60 -150 2.542741e-01 GT:PL:GQ 1/1:255,123,0:99

3 CHROM POS ID REF ALT U00096 73641 . A G

G missense_variant MODERATE thiP b0067 transcript AAC73178.1 Coding 1/1 c.881T>C p.Leu294Ser 881/1611 881/1611 294/536 U00096 gene 72911-

74521

- thiP b0067 yabK EcoGene:EG11573

U00096 CDS 72911- 74521

- thiP b0067 yabK EcoGene:EG11573 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0009228 - thiamin biosynthetic process 1 11 thiamine/thiamine pyrophosphate ABC transporter permease AAC73178.1

RESULTS_dnaQ

4 ^CHROM ^POS ^{ID REF ALT}

U00096 106233 . T C

C missense_variant MODERATE ftsZ b0095 transcript AAC73206.1 Coding 1/1 c.929T>C p.Val310Ala 929/1152 929/1152 310/383 U00096 gene 105305-

106456

+ ftsZ b0095 sulB EcoGene:EG10347

U00096 CDS 105305- 106456

+ ftsZ b0095 sulB EcoGene:EG10347 enzyme; Cell division cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase; GO_component: GO:0005737 - cytoplasm 1 11 GTP-binding tubulin-like cell division protein AAC73206.1 N-terminus verified by Edman degradation: PMID 9298646

RESULTS_dnaQ

5 ^CHROM ^POS ^{ID REF ALT}

U00096 109267 . A G

G missense_variant MODERATE secA b0098 transcript AAC73209.1 Coding 1/1 c.989A>G p.Asp330Gly 989/2706 989/2706 330/901 U00096 gene 108279-

110984

+ secA b0098 prlD EcoGene:EG10936

U00096 CDS 108279- 110984

+ secA b0098 prlD EcoGene:EG10936 transport; Protein, peptide secretion preprotein translocase; secretion protein;

GO_component: GO:0005737 - cytoplasm 1 11 preprotein translocase subunit, ATPase AAC73209.1 N-terminus verified by Edman degradation: PMID 2841285

(2)

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

6 ^CHROM ^POS ^{ID REF ALT}

U00096 141845 . G A

A missense_variant MODERATE hpt b0125 transcript AAC73236.2 Coding 1/1 c.415G>A p.Val139Ile 415/537 415/537 139/178

A downstream_gene_variant MODIFIER can b0126 transcript AAC73237.1 Coding c.*663C>T 163

U00096 gene 141431- 141967

+ hpt b0125 JW5009 EcoGene:EG20098

U00096 CDS 141431- 141967

+ hpt b0125 JW5009 EcoGene:EG20098 enzyme; Salvage of nucleosides and nucleotides GO_component: GO:0005737 - cytoplasm; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 hypoxanthine phosphoribosyltransferase AAC73236.2 2.4.2.8

RESULTS_dnaQ

7 ^CHROM ^POS ^{ID REF ALT}

U00096 150016 . T C

C missense_variant MODERATE yadC b0135 transcript AAC73246.1 Coding 1/1 c.938A>G p.Gln313Arg 938/1239 938/1239 313/412 U00096 gene 149715-

150953

- yadC b0135 JW0131 EcoGene:EG11678

U00096 CDS 149715- 150953

- yadC b0135 JW0131 EcoGene:EG11678 putative structural component; Surface structures putative fimbrial-like protein;

GO_component: GO:0009289 - pilus 1 11 putative fimbrial-like adhesin protein AAC73246.1

RESULTS_dnaQ

8 ^CHROM ^POS ^{ID REF ALT}

U00096 150562 . A G

G missense_variant MODERATE yadC b0135 transcript AAC73246.1 Coding 1/1 c.392T>C p.Ile131Thr 392/1239 392/1239 131/412 U00096 gene 149715-

150953

- yadC b0135 JW0131 EcoGene:EG11678

U00096 CDS 149715- 150953

- yadC b0135 JW0131 EcoGene:EG11678 putative structural component; Surface structures putative fimbrial-like protein;

RESULTS_dnaQ

9 ^CHROM ^POS ^ID ^REF ^ALT

U00096 152802 . GTTTTT GTTTT

frameshift_variant HIGH yadM b0138 transcript AAC73249.2 Coding 1/1 c.6delA p.Ile2fs 6/570 6/570 2/189

downstream_gene_variant MODIFIER htrE b0139 transcript AAC73250.1 Coding c.*2598delA 22

U00096 gene 152243- 152812

- yadM b0138 JW0134 EcoGene:EG12327

U00096 CDS 152243- 152812

- yadM b0138 JW0134 EcoGene:EG12327 putative structural component; Surface structures putative fimbrial-like protein;

RESULTS_dnaQ

10 ^CHROM ^POS ^{ID REF ALT}

U00096 152803 . T G

G missense_variant MODERATE yadM b0138 transcript AAC73249.2 Coding 1/1 c.10A>C p.Thr4Pro 10/570 10/570 4/189

G downstream_gene_variant MODIFIER htrE b0139 transcript AAC73250.1 Coding c.*2598A>C 26

U00096 gene 152243- 152812

- yadM b0138 JW0134 EcoGene:EG12327

(3)

U00096 CDS 152243- 152812

- yadM b0138 JW0134 EcoGene:EG12327 putative structural component; Surface structures putative fimbrial-like protein;

RESULTS_dnaQ

11 ^CHROM ^POS ^{ID REF ALT}

U00096 162249 . G A

A missense_variant MODERATE hrpB b0148 transcript AAC73259.2 Coding 1/1 c.145G>A p.Gly49Arg 145/2430 145/2430 49/809 U00096 gene 162105-

164534

+ hrpB b0148 yadO EcoGene:EG12329

U00096 CDS 162105- 164534

+ hrpB b0148 yadO EcoGene:EG12329 enzyme; DNA - replication, repair, restriction/modification helicase, ATP-dependent;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication 1 11 putative ATP-dependent helicase AAC73259.2

RESULTS_dnaQ

12 ^CHROM ^POS ^{ID REF ALT}

U00096 168919 . TGG TG

frameshift_variant HIGH fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1438delG p.Val480fs 1438/2244 1438/2244 480/747 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_CIQ1E 214.0 . 38 1 2 0,0,25,12 60 -146 2.711304e-02 35,0.921053 GT:PL:GQ 1/1:255,111,0:99

13 ^CHROM ^POS ^{ID REF ALT}

U00096 179605 . GTTT GTT

frameshift_variant HIGH dgt b0160 transcript AAC73271.1 Coding 1/1 c.372delT p.Phe124fs 372/1518 372/1518 124/505 U00096 gene 179237-

180754

+ dgt b0160 optA EcoGene:EG10225

U00096 CDS 179237- 180754

+ dgt b0160 optA EcoGene:EG10225 enzyme; Central intermediary metabolism: Nucleotide hydrolysis GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 deoxyguanosine triphosphate triphosphohydrolase AAC73271.1 3.1.5.1

RESULTS_dnaQ

14 ^CHROM ^POS ^{ID REF ALT}

U00096 179606 . T G

G missense_variant MODERATE dgt b0160 transcript AAC73271.1 Coding 1/1 c.370T>G p.Phe124Val 370/1518 370/1518 124/505 U00096 gene 179237-

180754

+ dgt b0160 optA EcoGene:EG10225

U00096 CDS 179237- 180754

+ dgt b0160 optA EcoGene:EG10225 enzyme; Central intermediary metabolism: Nucleotide hydrolysis GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 deoxyguanosine triphosphate triphosphohydrolase AAC73271.1 3.1.5.1

RESULTS_dnaQ

15 ^CHROM ^POS ^{ID REF ALT}

U00096 182578 . G A

A missense_variant MODERATE cdaR b0162 transcript AAC73273.2 Coding 1/1 c.116G>A p.Gly39Asp 116/1158 116/1158 39/385 U00096 gene 182463- + cdaR b0162 yaeG EcoGene:EG12335

(4)

183620 U00096 CDS 182463-

183620

+ cdaR b0162 yaeG EcoGene:EG12335 regulator; Not classified 1 11 carbohydrate diacid regulon transcriptional regulator; autoregulator AAC73273.2

RESULTS_dnaQ

16 ^CHROM ^POS ^{ID REF ALT}

U00096 192324 . A G

G missense_variant MODERATE pyrH b0171 transcript AAC73282.1 Coding 1/1 c.470A>G p.Glu157Gly 470/726 470/726 157/241 U00096 gene 191855-

192580

+ pyrH b0171 umk EcoGene:EG11539

U00096 CDS 191855- 192580

+ pyrH b0171 umk EcoGene:EG11539 enzyme; Central intermediary metabolism: Nucleotide interconversions GO_component: GO:0005737 - cytoplasm; GO_process: GO:0015949 - nucleobase, nucleoside and nucleotide interconversion 1 11 uridylate kinase AAC73282.1 2.7.4.-

RESULTS_dnaQ

17 ^CHROM ^POS ^{ID REF ALT}

U00096 207668 . C T

T missense_variant MODERATE dnaE b0184 transcript AAC73295.1 Coding 1/1 c.2543C>T p.Ala848Val 2543/3483 2543/3483 848/1160 U00096 gene 205126-

208608

+ dnaE b0184 sdgC EcoGene:EG10238

U00096 CDS 205126- 208608

+ dnaE b0184 sdgC EcoGene:EG10238 enzyme; DNA - replication, repair, restriction/modification DNA polymerase III, alpha subunit; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication 1 11 DNA polymerase III alpha subunit AAC73295.1 2.7.7.7

RESULTS_dnaQ

18 ^CHROM ^POS ^{ID REF ALT}

U00096 217355 . A G

G missense_variant MODERATE proS b0194 transcript AAC73305.1 Coding 1/1 c.1421T>C p.Phe474Ser 1421/1719 1421/1719 474/572 U00096 gene 217057-

218775

- proS b0194 JW0190 EcoGene:EG10770

U00096 CDS 217057- 218775

- proS b0194 JW0190 EcoGene:EG10770 enzyme; Aminoacyl tRNA synthetases, tRNA modification proline tRNA synthetase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006418 - tRNA aminoacylation for protein translation 1 11 prolyl-tRNA synthetase AAC73305.1 6.1.1.15 N-terminus verified by Edman degradation: PMID 2203971,9298646

RESULTS_dnaQ

19 ^CHROM ^POS ^{ID REF ALT}

U00096 229456 . A G

G missense_variant MODERATE dkgB b0207 transcript AAC73312.1 Coding 1/1 c.290A>G p.His97Arg 290/804 290/804 97/267 U00096 gene 229167-

229970

+ dkgB b0207 yafB EcoGene:EG11648

U00096 CDS 229167- 229970

+ dkgB b0207 yafB EcoGene:EG11648 putative enzyme; Not classified GO_component: GO:0005737 - cytoplasm;

GO_process: GO:0016052 - carbohydrate catabolic process 1 11 2,5-diketo-D-gluconate reductase B AAC73312.1 1.1.1.274

RESULTS_dnaQ

20 ^CHROM ^POS ^{ID REF ALT}

U00096 233268 . A G

G missense_variant MODERATE mltD b0211 transcript AAC73316.1 Coding 1/1 c.688T>C p.Tyr230His 688/1359 688/1359 230/452

(5)

U00096 gene 232597- 233955

- mltD b0211 yafG EcoGene:EG10246

U00096 CDS 232597- 233955

- mltD b0211 yafG EcoGene:EG10246 regulator; Energy metabolism, carbon: Anaerobic respiration GO_component:

GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity; GO_process: GO:0009061 - anaerobic respiration; GO_process: GO:0017004 - cytochrome complex assembly; GO_process: GO:0006350 - transcription 1 11 putative membrane-bound lytic murein transglycosylase D AAC73316.1 3.2.1.-

RESULTS_dnaQ

21 ^CHROM ^POS ^ID ^REF ^ALT

U00096 248368 . GCCCCC GCCCC

frameshift_variant HIGH lfhA b0229 transcript b0229 Coding 1/1 c.1698delG p.Met566fs 1698/1713 1698/1713 566/570 U00096 gene 248358-

250070

- lfhA b0229 JW5811 EcoGene:EG13144

U00096 CDS 248358- 250070

- lfhA b0229 JW5811 EcoGene:EG13144 pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis; GO_component: GO:0019861 - flagellum; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane 1 11

RESULTS_dnaQ

22 ^CHROM ^POS ^{ID REF ALT}

U00096 266547 . G T

T missense_variant MODERATE yafY b0251 transcript AAC73354.2 Coding 1/1 c.7C>A p.Arg3Ser 7/444 7/444 3/147

T downstream_gene_variant MODIFIER ykfL b4627 transcript b4627 Coding c.*222C>A 6

U00096 gene 266110- 266553

- yafY b0251 JW0240 EcoGene:EG13337

U00096 CDS 266110- 266553

- yafY b0251 JW0240 EcoGene:EG13337 Phage or Prophage Related hypothetical transcriptional regulator 1 11 lipoprotein, inner membrane; degP regulator; CP4-6 prophage AAC73354.2

RESULTS_dnaQ

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

U00096 278515 . TCCC TCC

frameshift_variant HIGH afuC b0262 transcript AAC73365.2 Coding 1/1 c.285delG p.Leu95fs 285/1047 285/1047 95/348 U00096 gene 277756-

278802

- afuC b0262 yagC EcoGene:EG12340

U00096 CDS 277756- 278802

- afuC b0262 yagC EcoGene:EG12340 putative transport; Not classified; Phage or Prophage Related putative ATP-binding component of a transport system 1 11 CP4-6 prophage; putative ferric transporter subunit AAC73365.2

RESULTS_dnaQ

24 ^CHROM ^POS ^{ID REF ALT}

U00096 281837 . C A

A missense_variant MODERATE yagA b0267 transcript AAC73370.1 Coding 1/1 c.147G>T p.Gln49His 147/1155 147/1155 49/384 U00096 gene 280829-

281983

- yagA b0267 JW0260 EcoGene:EG12338

U00096 CDS 280829- 281983

- yagA b0267 JW0260 EcoGene:EG12338 Phage or Prophage Related 1 11 CP4-6 prophage; putative DNA-binding transcriptional regulator AAC73370.1

RESULTS_dnaQ

25 ^CHROM ^POS ^{ID REF ALT}

U00096 293374 . A G

(6)

G missense_variant MODERATE yagL b0278 transcript AAC73381.1 Coding 1/1 c.545T>C p.Val182Ala 545/699 545/699 182/232 U00096 gene 293220-

293918

- yagL b0278 JW0272 EcoGene:EG13551

U00096 CDS 293220- 293918

- yagL b0278 JW0272 EcoGene:EG13551 Phage or Prophage Related DNA-binding protein 1 11 CP4-6 prophage;

DNA-binding protein AAC73381.1

RESULTS_dnaQ

26 ^CHROM ^POS ^{ID REF ALT}

U00096 319137 . C G

G missense_variant MODERATE rclA b0304 transcript AAC73407.2 Coding 1/1 c.865G>C p.Ala289Pro 865/1326 865/1326 289/441 U00096 gene 318676-

320001

- rclA b0304 ykgC EcoGene:EG13580

U00096 CDS 318676- 320001

- rclA b0304 ykgC EcoGene:EG13580 putative enzyme; Not classified putative oxidoreductase 1 11 reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide-dependent disulfide oxidoreductase family AAC73407.2

RESULTS_dnaQ

27 ^CHROM ^POS ^{ID REF ALT}

U00096 342381 . A C

C missense_variant MODERATE yahJ b0324 transcript AAC73427.1 Coding 1/1 c.1257A>C p.Lys419Asn 1257/1383 1257/1383 419/460 U00096 gene 341125-

342507

+ yahJ b0324 JW0316 EcoGene:EG13594

U00096 CDS 341125- 342507

+ yahJ b0324 JW0316 EcoGene:EG13594 putative enzyme; Not classified putative deaminase; GO_process: GO:0009310 - amine catabolic process 1 11 putative metallo-dependent hydrolase domain deaminase AAC73427.1

RESULTS_dnaQ

28 ^CHROM ^POS ^{ID REF ALT}

U00096 368027 . A G

G missense_variant MODERATE mhpR b0346 transcript AAC73449.2 Coding 1/1 c.394T>C p.Phe132Leu 394/834 394/834 132/277 U00096 gene 367587-

368420

- mhpR b0346 JW0337 EcoGene:EG20276

U00096 CDS 367587- 368420

- mhpR b0346 JW0337 EcoGene:EG20276 regulator; Not classified transcriptional regulator for mhp operon;

GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016563 - transcription activator activity; GO_process:

GO:0019395 - fatty acid oxidation; GO_process: GO:0006350 - transcription 1 11 mhp operon transcriptional activator AAC73449.2 N-terminus verified by Edman degradation: PMID 12748194

RESULTS_dnaQ

29 ^CHROM ^POS ^ID ^REF ^ALT

U00096 372462 . GCCC GCC

frameshift_variant HIGH mhpD b0350 transcript AAC73453.2 Coding 1/1 c.351delC p.Pro117fs 351/810 351/810 117/269 U00096 gene 372115-

372924

+ mhpD b0350 mhpS EcoGene:EG14274

U00096 CDS 372115- 372924

+ mhpD b0350 mhpS EcoGene:EG14274 enzyme; Degradation of small molecules: Carbon compounds GO_process:

GO:0019395 - fatty acid oxidation 1 11 2-keto-4-pentenoate hydratase AAC73453.2 4.2.1.80

RESULTS_dnaQ

30 ^CHROM ^POS ^{ID REF ALT}

U00096 372463 . C G

G missense_variant MODERATE mhpD b0350 transcript AAC73453.2 Coding 1/1 c.349C>G p.Pro117Ala 349/810 349/810 117/269

(7)

U00096 gene 372115- 372924

+ mhpD b0350 mhpS EcoGene:EG14274

U00096 CDS 372115- 372924

+ mhpD b0350 mhpS EcoGene:EG14274 enzyme; Degradation of small molecules: Carbon compounds GO_process:

GO:0019395 - fatty acid oxidation 1 11 2-keto-4-pentenoate hydratase AAC73453.2 4.2.1.80

RESULTS_dnaQ

RESULTS_CIQ1E 25.0 . 5 -1.291774e+00 0.5 1 2,1,0,2 60 28 0.4,1,1,1 5.960000e-02 GT:PL:GQ 0/1:55,0,89:58

31 ^CHROM ^POS ^{ID REF ALT}

U00096 387413 . T A

A missense_variant MODERATE tauC b0367 transcript AAC73470.1 Coding 1/1 c.443T>A p.Leu148Gln 443/828 443/828 148/275 U00096 gene 386971-

387798

+ tauC b0367 yaiJ EcoGene:EG13301

U00096 CDS 386971- 387798

+ tauC b0367 yaiJ EcoGene:EG13301 transport; Transport of small molecules: Amino acids, amines taurine transport system permease protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006790 - sulfur metabolic process; GO_process: GO:0009310 - amine catabolic process 1 11 taurine ABC transporter permease AAC73470.1

RESULTS_dnaQ

32 ^CHROM ^POS ^ID ^REF ^ALT

U00096 396813 . ATTTTTT ATTTTT

frameshift_variant HIGH sbmA b0377 transcript AAC73480.1 Coding 1/1 c.181delT p.Tyr61fs 181/1221 181/1221 61/406 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

33 ^CHROM ^POS ^{ID REF ALT}

U00096 396964 . A G

G missense_variant MODERATE sbmA b0377 transcript AAC73480.1 Coding 1/1 c.326A>G p.Asn109Ser 326/1221 326/1221 109/406 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

34 ^CHROM ^POS ^{ID REF ALT}

U00096 404920 . A G

G missense_variant MODERATE proC b0386 transcript AAC73489.1 Coding 1/1 c.725T>C p.Val242Ala 725/810 725/810 242/269

G downstream_gene_variant MODIFIER yaiC b0385 transcript AAC73488.1 Coding c.*1116A>G 102

U00096 gene 404835- 405644

- proC b0386 Pro2 EcoGene:EG10769

U00096 CDS 404835- 405644

- proC b0386 Pro2 EcoGene:EG10769 enzyme; Amino acid biosynthesis: Proline pyrroline-5-carboxylate reductase;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006561 - proline biosynthetic process 1 11 pyrroline-5- carboxylate reductase, NAD(P)-binding AAC73489.1 1.5.1.2 N-terminus verified by Edman degradation: PMID 6089111

RESULTS_dnaQ

35 ^CHROM ^POS ^{ID REF ALT}

U00096 405356 . C T

(8)

T missense_variant MODERATE proC b0386 transcript AAC73489.1 Coding 1/1 c.289G>A p.Ala97Thr 289/810 289/810 97/269 U00096 gene 404835-

405644

- proC b0386 Pro2 EcoGene:EG10769

U00096 CDS 404835- 405644

- proC b0386 Pro2 EcoGene:EG10769 enzyme; Amino acid biosynthesis: Proline pyrroline-5-carboxylate reductase;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006561 - proline biosynthetic process 1 11 pyrroline-5- carboxylate reductase, NAD(P)-binding AAC73489.1 1.5.1.2 N-terminus verified by Edman degradation: PMID 6089111

RESULTS_dnaQ

36 ^CHROM ^POS ^{ID REF ALT}

U00096 450100 . T C

C missense_variant MODERATE cyoB b0431 transcript AAC73534.1 Coding 1/1 c.542A>G p.Tyr181Cys 542/1992 542/1992 181/663 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

37 ^CHROM ^POS ^ID ^REF ^ALT

U00096 451585 . CTTTT CTTT

frameshift_variant HIGH cyoA b0432 transcript AAC73535.1 Coding 1/1 c.22delA p.Lys8fs 22/948 22/948 8/315 U00096 gene 450663-

451610

- cyoA b0432 JW0422 EcoGene:EG10178

U00096 CDS 450663- 451610

- cyoA b0432 JW0422 EcoGene:EG10178 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 II AAC73535.1 1.10.3.-

RESULTS_dnaQ

38 ^CHROM ^POS ^{ID REF ALT}

U00096 462215 . C A

A missense_variant MODERATE ppiD b0441 transcript AAC73544.1 Coding 1/1 c.301C>A p.Leu101Met 301/1872 301/1872 101/623 U00096 gene 461915-

463786

+ ppiD b0441 ybaU EcoGene:EG13249

U00096 CDS 461915- 463786

+ ppiD b0441 ybaU EcoGene:EG13249 putative factor; Not classified GO_process: GO:0006457 - protein folding 1 11 periplasmic folding chaperone, has an inactive PPIase domain AAC73544.1 5.2.1.8

RESULTS_dnaQ

39 ^CHROM ^POS ^{ID REF ALT}

U00096 471053 . G T

T missense_variant MODERATE mdlB b0449 transcript AAC73552.1 Coding 1/1 c.418G>T p.Val140Phe 418/1782 418/1782 140/593 U00096 gene 470636-

472417

+ mdlB b0449 mdl EcoGene:EG14374

U00096 CDS 470636- 472417

+ mdlB b0449 mdl EcoGene:EG14374 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 putative multidrug ABC transporter ATPase AAC73552.1

RESULTS_dnaQ

40 ^CHROM ^POS ^{ID REF ALT}

(9)

U00096 553240 . T C

C missense_variant MODERATE lpxH b0524 transcript AAC73626.1 Coding 1/1 c.701A>G p.Glu234Gly 701/723 701/723 234/240

C upstream_gene_variant MODIFIER purE b0523 transcript AAC73625.1 Coding c.-1A>G 140

U00096 gene 553218- 553940

- lpxH b0524 ybbF EcoGene:EG12666

U00096 CDS 553218- 553940

- lpxH b0524 ybbF EcoGene:EG12666 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_function:

GO:0042280 - cell surface antigen activity, host-interacting; GO_process: GO:0009245 - lipid A biosynthetic process 1 11 UDP-2,3-diacylglucosamine pyrophosphohydrolase AAC73626.1 3.6.1.-

RESULTS_dnaQ

41 ^CHROM ^POS ^{ID REF ALT}

U00096 560244 . A G

G missense_variant MODERATE sfmD b0532 transcript AAC73634.1 Coding 1/1 c.548A>G p.Asn183Ser 548/2604 548/2604 183/867 U00096 gene 559697-

562300

+ sfmD b0532 JW0521 EcoGene:EG13883

U00096 CDS 559697- 562300

+ sfmD b0532 JW0521 EcoGene:EG13883 membrane; Outer membrane constituents putative outer membrane protein, export function; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative outer membrane export usher protein AAC73634.1

RESULTS_dnaQ

42 ^CHROM ^POS ^ID ^REF ^ALT

U00096 583951 . GTTTTTT GTTTTT

frameshift_variant HIGH appY b0564 transcript AAC73665.1 Coding 1/1 c.277delT p.Ser93fs 277/750 277/750 93/249 U00096 gene 583681-

584430

+ appY b0564 JW0553 EcoGene:EG10050

U00096 CDS 583681- 584430

+ appY b0564 JW0553 EcoGene:EG10050 regulator; Central intermediary metabolism: Pool, multipurpose conversions;

Phage or Prophage Related regulatory protein affecting appA and other genes; GO_component: GO:0005737 - cytoplasm;

GO_function: GO:0016563 - transcription activator activity; GO_function: GO:0016564 - transcription repressor activity;

GO_process: GO:0006350 - transcription; GO_process: GO:0042594 - response to starvation 1 11 global transcriptional activator; DLP12 prophage AAC73665.1

RESULTS_dnaQ

43 ^CHROM ^POS ^{ID REF ALT}

U00096 585573 . A G

G missense_variant MODERATE ompT b0565 transcript AAC73666.1 Coding 1/1 c.61T>C p.Ser21Pro 61/954 61/954 21/317 U00096 gene 584680-

585633

- ompT b0565 JW0554 EcoGene:EG10673

U00096 CDS 584680- 585633

- ompT b0565 JW0554 EcoGene:EG10673 enzyme; Outer membrane constituents; Phage or Prophage Related outer membrane protein 3b (a), protease VII; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0009279 - cell outer membrane 1 11 DLP12 prophage; outer membrane protease VII; outer membrane protein 3b AAC73666.1 3.4.23.49

RESULTS_dnaQ

44 ^CHROM ^POS ^{ID REF ALT}

U00096 611479 . A G

G missense_variant MODERATE fepA b0584 transcript AAC73685.1 Coding 1/1 c.1016T>C p.Ile339Thr 1016/2241 1016/2241 339/746 U00096 gene 610254-

612494

- fepA b0584 JW5086 EcoGene:EG10293

U00096 CDS 610254- 612494

- fepA b0584 JW5086 EcoGene:EG10293 membrane; Transport of small molecules: Cations outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0009279 - cell outer membrane; GO_process: GO:0006826 - iron ion transport 1 11 ferrienterobactin outer membrane transporter AAC73685.1

(10)

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

RESULTS_CIQ1E 222.0 . 21 9.082951e-01 1 2 1,0,10,10 60 -52 1,0.28,1,1 1.981819e-01 GT:PL:GQ 1/1:255,25,0:47

45 ^CHROM ^POS ^{ID REF ALT}

U00096 635957 . A G

G missense_variant MODERATE ybdN b0602 transcript AAC73703.1 Coding 1/1 c.613T>C p.Tyr205His 613/1221 613/1221 205/406

U00096 gene 635349-636569 - ybdN b0602 JW0595 EcoGene:EG13533

U00096 CDS 635349-636569 - ybdN b0602 JW0595 EcoGene:EG13533 1 11 PAPS reductase-like domain protein AAC73703.1

RESULTS_dnaQ

46 ^CHROM ^POS ^{ID REF ALT}

U00096 636750 . G A

A missense_variant MODERATE ybdO b0603 transcript AAC73704.1 Coding 1/1 c.869C>T p.Ser290Phe 869/903 869/903 290/300

A upstream_gene_variant MODIFIER ybdN b0602 transcript AAC73703.1 Coding c.-1C>T 181

U00096 gene 636716- 637618

- ybdO b0603 JW0596 EcoGene:EG13534

U00096 CDS 636716- 637618

- ybdO b0603 JW0596 EcoGene:EG13534 putative regulator; Not classified putative transcriptional regulator LYSR-type;

GO_process: GO:0006350 - transcription; GO_process: GO:0006355 - regulation of transcription, DNA-dependent 1 11 putative DNA-binding transcriptional regulator AAC73704.1

RESULTS_dnaQ

47 ^CHROM ^POS ^{ID REF ALT}

U00096 642099 . GA G

frameshift_variant HIGH ybdR b0608 transcript AAC73709.1 Coding 1/1 c.13delA p.Thr5fs 13/1239 13/1239 5/412 U00096 gene 642088-

643326

+ ybdR b0608 JW0601 EcoGene:EG13537

U00096 CDS 642088- 643326

+ ybdR b0608 JW0601 EcoGene:EG13537 putative enzyme; Not classified putative oxidoreductase 1 11 putative Zn- dependent NAD(P)-binding oxidoreductase AAC73709.1

RESULTS_dnaQ

48 ^CHROM ^POS ^{ID REF ALT}

U00096 642100 . A C

C missense_variant MODERATE ybdR b0608 transcript AAC73709.1 Coding 1/1 c.13A>C p.Thr5Pro 13/1239 13/1239 5/412 U00096 gene 642088-

643326

U00096 CDS 642088- 643326

RESULTS_dnaQ

49 ^CHROM ^POS ^{ID REF ALT}

U00096 642101 . C T

T missense_variant MODERATE ybdR b0608 transcript AAC73709.1 Coding 1/1 c.14C>T p.Thr5Ile 14/1239 14/1239 5/412 U00096 gene 642088-

643326

U00096 CDS 642088- 643326

RESULTS_dnaQ

RESULTS_CIQ1E 41.0 . 21 3.000334e+00 0.5 1 8,9,3,1 60 44 0.59,1,1,7.8e-06 1.496627e-02 GT:PL:GQ 0/1:71,0,255:74

(11)

50 ^CHROM ^POS ^{ID REF ALT}

U00096 653615 . T C

C missense_variant MODERATE citA b0619 transcript AAC73720.1 Coding 1/1 c.1381T>C p.Phe461Leu 1381/1659 1381/1659 461/552 U00096 gene 652235-

653893

+ citA b0619 ybeP EcoGene:EG13646

U00096 CDS 652235- 653893

+ citA b0619 ybeP EcoGene:EG13646 regulator; Degradation of small molecules: Carbon compounds putative sensor-type protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006464 - protein modification process 1 11 sensory histidine kinase in two-component regulatory system with CitB AAC73720.1

RESULTS_dnaQ

51 ^CHROM ^POS ^{ID REF ALT}

U00096 673832 . T A

A missense_variant MODERATE leuS b0642 transcript AAC73743.1 Coding 1/1 c.952A>T p.Ile318Phe 952/2583 952/2583 318/860 U00096 gene 672201-

674783

- leuS b0642 JW0637 EcoGene:EG10532

U00096 CDS 672201- 674783

- leuS b0642 JW0637 EcoGene:EG10532 enzyme; Aminoacyl tRNA synthetases, tRNA modification leucine tRNA synthetase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006418 - tRNA aminoacylation for protein translation 1 11 leucyl-tRNA synthetase AAC73743.1 6.1.1.4 N-terminus verified by Edman degradation: PMID 3320963

RESULTS_dnaQ

52 ^CHROM ^POS ^{ID REF ALT}

U00096 692762 . ATTT ATT

frameshift_variant HIGH ybeZ b0660 transcript AAC73761.2 Coding 1/1 c.614delA p.Glu205fs 614/1041 614/1041 205/346 U00096 gene 692338-

693378

- ybeZ b0660 phoL EcoGene:EG13656

U00096 CDS 692338- 693378

- ybeZ b0660 phoL EcoGene:EG13656 putative ATP-binding protein in pho regulon 1 11 heat shock protein, putative NTPase; PhoH-like protein AAC73761.2

RESULTS_dnaQ

53 ^CHROM ^POS ^ID ^REF ^ALT

U00096 721881 . ACCCCC ACCCC

frameshift_variant HIGH kdpD b0695 transcript AAC73789.1 Coding 1/1 c.2529delG p.Pro843fs 2529/2685 2529/2685 843/894

upstream_gene_variant MODIFIER kdpE b0694 transcript AAC73788.1 Coding c.-1delG 153

U00096 gene 721730- 724414

- kdpD b0695 kac EcoGene:EG10516

U00096 CDS 721730- 724414

- kdpD b0695 kac EcoGene:EG10516 enzyme; Global regulatory functions sensor for high-affinity potassium transport system; sensory histidine kinase; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0006464 - protein modification process 1 11 fused sensory histidine kinase in two-component regulatory system with KdpE: signal sensing protein AAC73789.1

RESULTS_dnaQ

54 ^CHROM ^POS ^ID ^REF ^ALT

U00096 723863 . CGGGGG CGGGG

frameshift_variant HIGH kdpD b0695 transcript AAC73789.1 Coding 1/1 c.547delC p.Pro183fs 547/2685 547/2685 183/894 U00096 gene 721730-

724414

U00096 CDS 721730- 724414

(12)

RESULTS_dnaQ

55 ^CHROM ^POS ^{ID REF ALT}

U00096 723864 . G C

C missense_variant MODERATE kdpD b0695 transcript AAC73789.1 Coding 1/1 c.551C>G p.Pro184Arg 551/2685 551/2685 184/894 U00096 gene 721730-

724414

U00096 CDS 721730- 724414

RESULTS_dnaQ

RESULTS_CIQ1E 59.0 . 5 -1.291774e+00 0.5 1 2,0,1,2 60 28 0.4,0.25,1,0.014 2.063840e-02 GT:PL:GQ 0/1:89,0,55:58

56 ^CHROM ^POS ^ID ^REF ^ALT

U00096 742309 . GCCCCC GCCCC

frameshift_variant HIGH dtpD b0709 transcript AAC73803.1 Coding 1/1 c.243delG p.Leu81fs 243/1482 243/1482 81/493 U00096 gene 741075-

742556

- dtpD b0709 ybgH EcoGene:EG13304

U00096 CDS 741075- 742556

- dtpD b0709 ybgH EcoGene:EG13304 transport; Not classified putative transport protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 dipeptide and tripeptide permease D AAC73803.1

RESULTS_dnaQ

57 ^CHROM ^POS ^{ID REF ALT}

U00096 751308 . C T

T missense_variant MODERATE ybgQ b0718 transcript AAC73812.2 Coding 1/1 c.862G>A p.Val288Ile 862/2448 862/2448 288/815 U00096 gene 749722-

752169

- ybgQ b0718 JW5099 EcoGene:EG13313

U00096 CDS 749722- 752169

- ybgQ b0718 JW5099 EcoGene:EG13313 putative membrane; Not classified GO_component: GO:0009274 -

peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative outer membrane protein AAC73812.2

RESULTS_dnaQ

58 ^CHROM ^POS ^{ID REF ALT}

U00096 753415 . A G

G missense_variant MODERATE gltA b0720 transcript AAC73814.1 Coding 1/1 c.1054T>C p.Tyr352His 1054/1284 1054/1284 352/427 U00096 gene 753185-

754468

- gltA b0720 JW0710 EcoGene:EG10402

U00096 CDS 753185- 754468

- gltA b0720 JW0710 EcoGene:EG10402 enzyme; Energy metabolism, carbon: TCA cycle GO_process: GO:0006099 - tricarboxylic acid cycle; GO_process: GO:0009061 - anaerobic respiration 1 11 citrate synthase AAC73814.1 2.3.3.1

RESULTS_dnaQ

59 ^CHROM ^POS ^{ID REF ALT}

U00096 808026 . T C

C missense_variant MODERATE bioA b0774 transcript AAC73861.1 Coding 1/1 c.1232A>G p.Gln411Arg 1232/1290 1232/1290 411/429

C upstream_gene_variant MODIFIER ybhB b0773 transcript AAC73860.1 Coding c.-1A>G 117

(13)

U00096 gene 807968- 809257

- bioA b0774 JW0757 EcoGene:EG10117

U00096 CDS 807968- 809257

- bioA b0774 JW0757 EcoGene:EG10117 enzyme; Biosynthesis of cofactors, carriers: Biotin 7,8-diaminopelargonic acid synthetase; GO_process: GO:0009102 - biotin biosynthetic process 1 11 7,8-diaminopelargonic acid synthase, PLP- dependent AAC73861.1 2.6.1.62

RESULTS_dnaQ

60 ^CHROM ^POS ^{ID REF ALT}

U00096 814361 . A G

G missense_variant MODERATE uvrB b0779 transcript AAC73866.1 Coding 1/1 c.836A>G p.Lys279Arg 836/2022 836/2022 279/673 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

61 ^CHROM ^POS ^ID ^REF ^ALT

U00096 819060 . CTTTTTTT CTTTTTTTT

T frameshift_variant HIGH moaD b0784 transcript AAC73871.1 Coding 1/1 c.20dupT p.Ala8fs 21/246 21/246 7/81

T downstream_gene_variant MODIFIER moaC b0783 transcript AAC73870.1 Coding c.*486dupT 13

U00096 gene 819048- 819293

+ moaD b0784 JW0767 EcoGene:EG11597

U00096 CDS 819048- 819293

+ moaD b0784 JW0767 EcoGene:EG11597 enzyme; Biosynthesis of cofactors, carriers: Molybdopterin molybdopterin biosynthesis; GO_process: GO:0006777 - Mo-molybdopterin cofactor biosynthetic process 1 11 molybdopterin synthase, small subunit AAC73871.1 N-terminus verified by Edman degradation: PMID 8514782

RESULTS_dnaQ

62 ^CHROM ^POS ^ID ^REF ^ALT

U00096 844959 . ATTTTTTT ATTTTTTTT

T frameshift_variant HIGH ybiO b0808 transcript AAC73895.2 Coding 1/1 c.514_515insA p.Lys173fs 514/2226 514/2226 172/741 U00096 gene 843255-

845480

- ybiO b0808 JW5108 EcoGene:EG13320

U00096 CDS 843255- 845480

- ybiO b0808 JW5108 EcoGene:EG13320 putative transport; Not classified putative transport protein 1 11 mechanosensitive channel protein, intermediate conductance AAC73895.2

RESULTS_dnaQ

63 ^CHROM ^POS ^ID ^REF ^ALT

U00096 868414 . GCCCCCCCC GCCCCCCC

frameshift_variant HIGH gsiA b0829 transcript AAC73916.2 Coding 1/1 c.903delC p.Pro301fs 903/1872 903/1872 301/623 U00096 gene 867520-

869391

+ gsiA b0829 yliA EcoGene:EG13472

U00096 CDS 867520- 869391

+ gsiA b0829 yliA EcoGene:EG13472 putative transport; Not classified putative ATP-binding component of a transport system; GO_component: GO:0005737 - cytoplasm 1 11 glutathione ABC transporter ATPase AAC73916.2

RESULTS_dnaQ

64 ^CHROM ^POS ^ID ^REF ^ALT

U00096 872427 . GCCC GCC

(14)

frameshift_variant HIGH gsiD b0832 transcript AAC73919.1 Coding 1/1 c.541delC p.Arg181fs 541/912 541/912 181/303 U00096 gene 871890-

872801

+ gsiD b0832 yliD EcoGene:EG13475

U00096 CDS 871890- 872801

+ gsiD b0832 yliD EcoGene:EG13475 putative transport; Not classified putative transport system permease protein;

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 glutathione ABC transporter permease AAC73919.1

RESULTS_dnaQ

65 ^CHROM ^POS ^{ID REF ALT}

U00096 872428 . C G

G missense_variant MODERATE gsiD b0832 transcript AAC73919.1 Coding 1/1 c.539C>G p.Ala180Gly 539/912 539/912 180/303 U00096 gene 871890-

872801

+ gsiD b0832 yliD EcoGene:EG13475

U00096 CDS 871890- 872801

+ gsiD b0832 yliD EcoGene:EG13475 putative transport; Not classified putative transport system permease protein;

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 glutathione ABC transporter permease AAC73919.1

RESULTS_dnaQ

RESULTS_CIQ1E 100.0 . 9 -2.240820e+00 0.5 1 2,2,3,2 60 67 1,1,1,0.47 9.843946e-03 GT:PL:GQ 0/1:130,0,94:97

66 ^CHROM ^POS ^{ID REF ALT}

U00096 881661 . T G

G missense_variant MODERATE dacC b0839 transcript AAC73926.1 Coding 1/1 c.935T>G p.Leu312Arg 935/1203 935/1203 312/400 U00096 gene 880727-

881929

+ dacC b0839 JW0823 EcoGene:EG10203

U00096 CDS 880727- 881929

+ dacC b0839 JW0823 EcoGene:EG10203 enzyme; Murein sacculus, peptidoglycan D-alanyl-D-alanine carboxypeptidase;

penicillin-binding protein 6; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0042493 - response to drug 1 11 D-alanyl-D-alanine carboxypeptidase; penicillin-binding protein 6a AAC73926.1 3.4.16.4

RESULTS_dnaQ

67 ^CHROM ^POS ^{ID REF ALT}

U00096 885221 . T C

C missense_variant MODERATE ybjH b0843 transcript AAC73930.1 Coding 1/1 c.10A>G p.Lys4Glu 10/285 10/285 4/94

C downstream_gene_variant MODIFIER ybjI b0844 transcript AAC73931.2 Coding c.*816A>G 95

U00096 gene 884946-885230 - ybjH b0843 JW0827 EcoGene:EG13677

U00096 CDS 884946-885230 - ybjH b0843 JW0827 EcoGene:EG13677 1 11 uncharacterized protein AAC73930.1

RESULTS_dnaQ

68 ^CHROM ^POS ^{ID REF ALT}

U00096 934494 . C T

T missense_variant MODERATE ftsK b0890 transcript AAC73976.1 Coding 1/1 c.1271C>T p.Ala424Val 1271/3990 1271/3990 424/1329 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

69 ^CHROM ^POS ^{ID REF ALT}

U00096 941442 . T G

(15)

G missense_variant MODERATE dmsA b0894 transcript AAC73980.2 Coding 1/1 c.484T>G p.Ser162Ala 484/2445 484/2445 162/814 U00096 gene 940959-

943403

+ dmsA b0894 JW5118 EcoGene:EG10232

U00096 CDS 940959- 943403

+ dmsA b0894 JW5118 EcoGene:EG10232 enzyme; Energy metabolism, carbon: Anaerobic respiration anaerobic dimethyl sulfoxide reductase subunit A; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0009061 - anaerobic respiration 1 11 dimethyl sulfoxide reductase, anaerobic, subunit A AAC73980.2 1.8.99.-

RESULTS_dnaQ

70 ^CHROM ^POS ^{ID REF ALT}

U00096 949466 . T C

C missense_variant MODERATE ycaN b0900 transcript AAC73986.1 Coding 1/1 c.103A>G p.Ser35Gly 103/909 103/909 35/302 U00096 gene 948660-

949568

- ycaN b0900 JW0883 EcoGene:EG13698

U00096 CDS 948660- 949568

- ycaN b0900 JW0883 EcoGene:EG13698 putative regulator; Not classified putative transcriptional regulator LYSR-type;

GO_function: GO:0016563 - transcription activator activity; GO_function: GO:0016564 - transcription repressor activity;

GO_process: GO:0006350 - transcription 1 11 LysR family putative transcriptional regulator AAC73986.1

RESULTS_dnaQ

71 ^CHROM ^POS ^{ID REF ALT}

U00096 978267 . G A

A missense_variant MODERATE mukB b0924 transcript AAC74010.1 Coding 1/1 c.1942G>A p.Glu648Lys 1942/4461 1942/4461 648/1486 U00096 gene 976326-

980786

+ mukB b0924 JW0907 EcoGene:EG10618

U00096 CDS 976326- 980786

+ mukB b0924 JW0907 EcoGene:EG10618 structural component; Cell division kinesin-like cell division protein involved in chromosome partitioning 1 11 chromosome condensin MukBEF, ATPase and DNA-binding subunit AAC74010.1 N- terminus verified by Edman degradation: PMID 1464330

RESULTS_dnaQ

72 ^CHROM ^POS ^{ID REF ALT}

U00096 982788 . T C

C missense_variant MODERATE ldtD b0925 transcript AAC74011.1 Coding 1/1 c.1742T>C p.Val581Ala 1742/1848 1742/1848 581/615 U00096 gene 981047-

982894

+ ldtD b0925 ycbB EcoGene:EG11253

U00096 CDS 981047- 982894

+ ldtD b0925 ycbB EcoGene:EG11253 enzyme; Murein sacculus, peptidoglycan putative amidase 1 11 murein L,D- transpeptidase AAC74011.1

RESULTS_dnaQ

73 ^CHROM ^POS ^{ID REF ALT}

U00096 989174 . G A

A missense_variant MODERATE pncB b0931 transcript AAC74017.1 Coding 1/1 c.1183C>T p.His395Tyr 1183/1203 1183/1203 395/400

A upstream_gene_variant MODIFIER asnS b0930 transcript AAC74016.1 Coding c.-1C>T 189

U00096 gene 989154- 990356

- pncB b0931 JW0914 EcoGene:EG10742

U00096 CDS 989154- 990356

- pncB b0931 JW0914 EcoGene:EG10742 enzyme; Biosynthesis of cofactors, carriers: Pyridine nucleotide GO_component:

GO:0042597 - periplasmic space; GO_process: GO:0009435 - NAD biosynthetic process 1 11 nicotinate phosphoribosyltransferase AAC74017.1 6.3.4.21

RESULTS_dnaQ

CHROM POS ID REF ALT

(16)

74 U00096 995400 . A G

G missense_variant MODERATE ssuD b0935 transcript AAC74021.1 Coding 1/1 c.589T>C p.Trp197Arg 589/1146 589/1146 197/381 U00096 gene 994843-

995988

- ssuD b0935 ycbN EcoGene:EG13706

U00096 CDS 994843- 995988

- ssuD b0935 ycbN EcoGene:EG13706 GO_process: GO:0006790 - sulfur metabolic process 1 11 alkanesulfonate monooxygenase, FMNH(2)-dependent AAC74021.1 1.14.14.5

RESULTS_dnaQ

75 ^CHROM ^POS ^{ID REF ALT}

U00096 997898 . A G

G missense_variant MODERATE elfA b0938 transcript AAC74024.2 Coding 1/1 c.31A>G p.Thr11Ala 31/540 31/540 11/179 U00096 gene 997868-

998407

+ elfA b0938 ycbQ EcoGene:EG13709

U00096 CDS 997868- 998407

+ elfA b0938 ycbQ EcoGene:EG13709 structural component; Surface structures putative fimbrial-like protein;

GO_component: GO:0009289 - pilus 1 11 laminin-binding fimbrin subunit AAC74024.2

RESULTS_dnaQ

76 ^CHROM ^POS ^{ID REF ALT}

U00096 1019171 . T A

A missense_variant MODERATE ompA b0957 transcript AAC74043.1 Coding 1/1 c.883A>T p.Ile295Phe 883/1041 883/1041 295/346 U00096 gene 1019013-

1020053

- ompA b0957 tut EcoGene:EG10669

U00096 CDS 1019013- 1020053

- ompA b0957 tut EcoGene:EG10669 membrane; Outer membrane constituents outer membrane protein 3a (II*;G;d);

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 outer membrane protein A (3a;II*;G;d) AAC74043.1

RESULTS_dnaQ

77 ^CHROM ^POS ^{ID REF ALT}

U00096 1046805 . T G

G missense_variant MODERATE gfcD b0984 transcript AAC74069.1 Coding 1/1 c.1141A>C p.Thr381Pro 1141/2097 1141/2097 381/698 U00096 gene 1045849-

1047945

- gfcD b0984 ymcA EcoGene:EG13729

U00096 CDS 1045849- 1047945

- gfcD b0984 ymcA EcoGene:EG13729 1 11 putative O-antigen capsule production periplasmic protein AAC74069.1

RESULTS_dnaQ

78 ^CHROM ^POS ^{ID REF ALT}

U00096 1065263 . C T

T missense_variant MODERATE yccE b1001 transcript AAC74086.1 Coding 1/1 c.1228C>T p.Leu410Phe 1228/1257 1228/1257 410/418 U00096 gene 1064036-1065292 + yccE b1001 JW0986 EcoGene:EG12196

U00096 CDS 1064036-1065292 + yccE b1001 JW0986 EcoGene:EG12196 1 11 uncharacterized protein AAC74086.1

RESULTS_dnaQ

79 ^CHROM ^POS ^{ID REF ALT}

U00096 1065984 . A G

G missense_variant MODERATE agp b1002 transcript AAC74087.1 Coding 1/1 c.400A>G p.Ile134Val 400/1242 400/1242 134/413

Non synonimous mutations found in sample: CIQ1E