Non synonimous mutations found in sample: CIQ4J

(1)

Non synonimous mutations found in sample: CIQ4J

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 37137 . A C

C missense_variant MODERATE caiC b0037 transcript AAC73148.2 Coding 1/1 c.688T>G p.Cys230Gly 688/1554 688/1554 230/517 U00096 gene 36271-

37824

- caiC b0037 yaaM EcoGene:EG11558

U00096 CDS 36271- 37824

- caiC b0037 yaaM EcoGene:EG11558 putative enzyme; Central intermediary metabolism: Pool, multipurpose conversions probable crotonobetaine/carnitine-CoA ligase; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009310 - amine catabolic process 1 11 putative crotonobetaine/carnitine-CoA ligase AAC73148.2 6.3.2.-

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

RESULTS_dnaQ

RESULTS_CIQ4J 222.0 . 48 1 2 0,0,16,31 60 -168 3.547089e-01 GT:PL:GQ 1/1:255,141,0:99

2 CHROM POS ID REF ALT U00096 42758 . GC G

frameshift_variant HIGH fixA b0041 transcript AAC73152.2 Coding 1/1 c.357delC p.Gly119fs 357/771 357/771 119/256 U00096 gene 42403-

43173

+ fixA b0041 yaaQ EcoGene:EG11562

U00096 CDS 42403- 43173

+ fixA b0041 yaaQ EcoGene:EG11562 putative enzyme; Energy metabolism, carbon: Electron transport probable flavoprotein subunit, carnitine metabolism; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 anaerobic carnitine reduction putative electron transfer flavoprotein subunit AAC73152.2

RESULTS_dnaQ

RESULTS_CIQ4J 214.0 . 44 1 2 0,0,17,23 60 -155 1.017157e-01 38,0.863636 GT:PL:GQ 1/1:255,120,0:99

3 CHROM POS ID REF ALT U00096 54435 . T C

C missense_variant MODERATE surA b0053 transcript AAC73164.1 Coding 1/1 c.268A>G p.Lys90Glu 268/1287 268/1287 90/428 U00096 gene 53416-

54702

- surA b0053 JW0052 EcoGene:EG10985

U00096 CDS 53416- 54702

- surA b0053 JW0052 EcoGene:EG10985 phenotype; Not classified survival protein; GO_component: GO:0009279 - cell outer membrane; GO_process: GO:0006457 - protein folding 1 11 peptidyl-prolyl cis-trans isomerase (PPIase) AAC73164.1 5.2.1.8

RESULTS_dnaQ

4 CHROM POS ID REF ALT U00096 61164 . C T

T missense_variant MODERATE rapA b0059 transcript AAC73170.1 Coding 1/1 c.2101G>A p.Ala701Thr 2101/2907 2101/2907 701/968 U00096 gene 60358-

63264

- rapA b0059 yabA EcoGene:EG11083

U00096 CDS 60358- 63264

- rapA b0059 yabA EcoGene:EG11083 putative enzyme; RNA synthesis, modification, DNA transcription probable ATP- dependent RNA helicase; GO_process: GO:0009451 - RNA modification 1 11 RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated, ATP-dependent RNA translocase AAC73170.1 3.6.1.-

RESULTS_dnaQ

5 ^CHROM ^POS ^{ID REF ALT}

U00096 106741 . T G

G missense_variant MODERATE lpxC b0096 transcript AAC73207.1 Coding 1/1 c.185T>G p.Leu62Arg 185/918 185/918 62/305 U00096 gene 106557-

107474

+ lpxC b0096 JW0094 EcoGene:EG10265

(2)

U00096 CDS 106557- 107474

+ lpxC b0096 JW0094 EcoGene:EG10265 enzyme; Surface polysaccharides & antigens UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0005737 - cytoplasm; GO_function: GO:0042280 - cell surface antigen activity, host-interacting; GO_process:

GO:0009245 - lipid A biosynthetic process 1 11 UDP-3-O-acyl N-acetylglucosamine deacetylase AAC73207.1 3.5.1.- N- terminus verified by Edman degradation: PMID 8530464

RESULTS_dnaQ

RESULTS_CIQ4J 222.0 . 36 -1.540195e+00 1 2 1,0,18,17 60 -97 1,0.33,1,1 2.753619e-01 GT:PL:GQ 1/1:255,70,0:99

6 ^CHROM ^POS ^{ID REF ALT}

U00096 143125 . G A

A missense_variant MODERATE yadG b0127 transcript AAC73238.1 Coding 1/1 c.347G>A p.Arg116His 347/927 347/927 116/308 U00096 gene 142779-

143705

+ yadG b0127 JW0123 EcoGene:EG12320

U00096 CDS 142779- 143705

+ yadG b0127 JW0123 EcoGene:EG12320 putative transport; Not classified putative ATP-binding component of a transport system; GO_component: GO:0005737 - cytoplasm 1 11 putative ABC transporter ATPase AAC73238.1

RESULTS_dnaQ

7 ^CHROM ^POS ^{ID REF ALT}

U00096 153179 . C T

T missense_variant MODERATE htrE b0139 transcript AAC73250.1 Coding 1/1 c.2248G>A p.Val750Ile 2248/2598 2248/2598 750/865 U00096 gene 152829-

155426

- htrE b0139 JW0135 EcoGene:EG11972

U00096 CDS 152829- 155426

- htrE b0139 JW0135 EcoGene:EG11972 putative membrane; Surface structures probable outer membrane porin protein involved in fimbrial assembly; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative outer membrane usher protein AAC73250.1

RESULTS_dnaQ

8 ^CHROM ^POS ^ID ^REF ^ALT

U00096 156192 . TAAAAAA TAAAAA

frameshift_variant HIGH yadV b0140 transcript AAC73251.1 Coding 1/1 c.4delT p.Phe2fs 4/741 4/741 2/246

downstream_gene_variant MODIFIER yadN b0141 transcript AAC73252.1 Coding c.*585delT 101

U00096 gene 155461- 156201

- yadV b0140 JW0136 EcoGene:EG11973

U00096 CDS 155461- 156201

- yadV b0140 JW0136 EcoGene:EG11973 putative factor; Surface structures probable pilin chaperone similar to PapD;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006457 - protein folding 1 11 putative periplasmic pilin chaperone AAC73251.1

RESULTS_dnaQ

RESULTS_CIQ4J 88.5 . 14 1 2 0,0,6,6 58 -70.5 3.760116e-02 12,0.857143 GT:PL:GQ 1/1:129,36,0:69

9 ^CHROM ^POS ^ID ^REF ^ALT

U00096 167646 . TGGGGG TGGGG

frameshift_variant HIGH fhuA b0150 transcript AAC73261.1 Coding 1/1 c.168delG p.Gly56fs 168/2244 168/2244 56/747 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

10 ^CHROM ^POS ^{ID REF ALT}

U00096 196002 . C T

(3)

T missense_variant MODERATE cdsA b0175 transcript AAC73286.2 Coding 1/1 c.326C>T p.Ser109Phe 326/858 326/858 109/285 U00096 gene 195677-

196534

+ cdsA b0175 JW5810 EcoGene:EG10139

U00096 CDS 195677- 196534

+ cdsA b0175 JW5810 EcoGene:EG10139 enzyme; Fatty acid and phosphatidic acid biosynthesis CDP-diglyceride synthetase; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0008654 - phospholipid biosynthetic process 1 11 CDP-diglyceride synthase AAC73286.2 2.7.7.41

RESULTS_dnaQ

RESULTS_CIQ4J 222.0 . 36 -1.251408e+00 1 2 1,0,15,20 60 -97 0.44,0.33,1,1 2.489355e-01 GT:PL:GQ 1/1:255,70,0:99

11 ^CHROM ^POS ^{ID REF ALT}

U00096 199378 . G A

A missense_variant MODERATE bamA b0177 transcript AAC73288.1 Coding 1/1 c.1451G>A p.Ser484Asn 1451/2433 1451/2433 484/810 U00096 gene 197928-

200360

+ bamA b0177 yzzY EcoGene:EG12676

U00096 CDS 197928- 200360

+ bamA b0177 yzzY EcoGene:EG12676 putative outer membrane antigen; GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor AAC73288.1

RESULTS_dnaQ

12 ^CHROM ^POS ^{ID REF ALT}

U00096 236071 . G T

T missense_variant MODERATE dnaQ b0215 transcript AAC73320.1 Coding 1/1 c.5G>T p.Ser2Ile 5/732 5/732 2/243

T upstream_gene_variant MODIFIER rnhA b0214 transcript AAC73319.1 Coding c.-1C>A 69

U00096 gene 236067- 236798

+ dnaQ b0215 mutD EcoGene:EG10243

U00096 CDS 236067- 236798

+ dnaQ b0215 mutD EcoGene:EG10243 enzyme; DNA - replication, repair, restriction/modification DNA polymerase III, epsilon subunit; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication;

GO_process: GO:0006457 - protein folding 1 11 DNA polymerase III epsilon subunit AAC73320.1 2.7.7.7

RESULTS_dnaQ

RESULTS_CIQ4J 5.46 . 1 1 2 0,0,0,1 60 -30 GT:PL:GQ 1/1:34,3,0:3

13 ^CHROM ^POS ^{ID REF ALT}

U00096 239682 . A C

C missense_variant MODERATE yafV b0219 transcript AAC73323.1 Coding 1/1 c.508T>G p.Ser170Ala 508/771 508/771 170/256 U00096 gene 239419-

240189

- yafV b0219 JW5019 EcoGene:EG13334

U00096 CDS 239419- 240189

- yafV b0219 JW5019 EcoGene:EG13334 putative enzyme; Not classified putative EC 3.5. amidase-type enzyme 1 11 putative NAD(P)-binding C-N hydrolase family amidase AAC73323.1

RESULTS_dnaQ

14 ^CHROM ^POS ^{ID REF ALT}

U00096 287376 . G A

A stop_gained HIGH yagH b0271 transcript AAC73374.1 Coding 1/1 c.588G>A p.Trp196* 588/1611 588/1611 196/536 U00096 gene 286789-

288399

+ yagH b0271 JW0264 EcoGene:EG13347

U00096 CDS 286789- 288399

+ yagH b0271 JW0264 EcoGene:EG13347 Phage or Prophage Related putative beta-xylosidase 1 11 CP4-6 prophage;

putative xylosidase/arabinosidase AAC73374.1

RESULTS_dnaQ

15 ^CHROM ^POS ^{ID REF ALT}

U00096 291906 . C T

(4)

T missense_variant MODERATE yagJ b0276 transcript b0276 Coding 1/1 c.503C>T p.Ser168Leu 503/828 503/828 168/275 U00096 gene 291404-

292231

+ yagJ b0276 JW0270 EcoGene:EG13549

U00096 CDS 291404- 292231

+ yagJ b0276 JW0270 EcoGene:EG13549 CP4-6 prophage; uncharacterized protein;Phage or Prophage Related 1 11

RESULTS_dnaQ

16 ^CHROM ^POS ^ID ^REF ^ALT

U00096 308982 . CGGGG CGGG

frameshift_variant HIGH ecpC b0291 transcript AAC73394.1 Coding 1/1 c.347delC p.Ala116fs 347/2526 347/2526 116/841 U00096 gene 306807-

309332

- ecpC b0291 yagX EcoGene:EG13563

U00096 CDS 306807- 309332

- ecpC b0291 yagX EcoGene:EG13563 membrane; Outer membrane constituents putative enzyme 1 11 ECP production outer membrane protein AAC73394.1

RESULTS_dnaQ

17 ^CHROM ^POS ^{ID REF ALT}

U00096 308983 . G C

C missense_variant MODERATE ecpC b0291 transcript AAC73394.1 Coding 1/1 c.350C>G p.Pro117Arg 350/2526 350/2526 117/841 U00096 gene 306807-

309332

- ecpC b0291 yagX EcoGene:EG13563

U00096 CDS 306807- 309332

- ecpC b0291 yagX EcoGene:EG13563 membrane; Outer membrane constituents putative enzyme 1 11 ECP production outer membrane protein AAC73394.1

RESULTS_dnaQ

18 ^CHROM ^POS ^{ID REF ALT}

U00096 321002 . C T

T missense_variant MODERATE rclR b0305 transcript AAC73408.1 Coding 1/1 c.776C>T p.Ser259Phe 776/855 776/855 259/284 U00096 gene 320227-

321081

+ rclR b0305 ykgD EcoGene:EG13581

U00096 CDS 320227- 321081

+ rclR b0305 ykgD EcoGene:EG13581 regulator; Not classified putative ARAC-type regulatory protein; GO_function:

GO:0016563 - transcription activator activity; GO_process: GO:0006350 - transcription 1 11 reactive chlorine species (RCS)-specific activator of the rcl genes AAC73408.1

RESULTS_dnaQ

19 ^CHROM ^POS ^ID ^REF ^ALT

U00096 333702 . CAAAAAA CAAAAAAA

A frameshift_variant HIGH yahB b0316 transcript AAC73419.1 Coding 1/1 c.725_726insT p.Phe243fs 725/933 725/933 242/310 U00096 gene 333501-

334433

- yahB b0316 JW0308 EcoGene:EG13586

U00096 CDS 333501- 334433

- yahB b0316 JW0308 EcoGene:EG13586 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 putative DNA-bindng transcriptional regulator AAC73419.1

RESULTS_dnaQ

20 ^CHROM ^POS ^ID ^REF ^ALT

U00096 397556 . GAAAAA GAAAAAA

(5)

A frameshift_variant HIGH sbmA b0377 transcript AAC73480.1 Coding 1/1 c.923dupA p.Asn308fs 924/1221 924/1221 308/406 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

21 ^CHROM ^POS ^{ID REF ALT}

U00096 401507 . C T

T missense_variant MODERATE iraP b0382 transcript AAC73485.1 Coding 1/1 c.122C>T p.Ala41Val 122/261 122/261 41/86 U00096 gene 401386-

401646

+ iraP b0382 yaiB EcoGene:EG11256

U00096 CDS 401386- 401646

+ iraP b0382 yaiB EcoGene:EG11256 1 11 anti-RssB factor, RpoS stabilzer during Pi starvation; anti-adapter protein AAC73485.1

RESULTS_dnaQ

22 ^CHROM ^POS ^{ID REF ALT}

U00096 427572 . G A

A missense_variant MODERATE yajC b0407 transcript AAC73510.1 Coding 1/1 c.286G>A p.Asp96Asn 286/333 286/333 96/110

A upstream_gene_variant MODIFIER secD b0408 transcript AAC73511.1 Coding c.-1G>A 75

U00096 gene 427287- 427619

+ yajC b0407 JW0397 EcoGene:EG11096

U00096 CDS 427287- 427619

+ yajC b0407 JW0397 EcoGene:EG11096 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 SecYEG protein translocase auxillary subunit AAC73510.1

RESULTS_dnaQ

23 ^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

24 ^CHROM ^POS ^{ID REF ALT}

U00096 459044 . G A

A missense_variant MODERATE lon b0439 transcript AAC73542.1 Coding 1/1 c.157G>A p.Val53Ile 157/2355 157/2355 53/784 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

25 ^CHROM ^POS ^ID ^REF ^ALT

(6)

U00096 469563 . CAAAAAAAA CAAAAAAAAA

A frameshift_variant HIGH mdlA b0448 transcript AAC73551.1 Coding 1/1 c.701dupA p.Asn234fs 702/1773 702/1773 234/590 U00096 gene 468871-

470643

+ mdlA b0448 mdl EcoGene:EG11622

U00096 CDS 468871- 470643

+ mdlA b0448 mdl EcoGene:EG11622 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0042493 - response to drug 1 11 putative multidrug ABC transporter ATPase AAC73551.1

RESULTS_dnaQ

RESULTS_CIQ4J 59.5 . 39 1 2 1,1,19,15 60 -114 1,1,1,1 1.571011e-01 31,0.794872 GT:PL:GQ 1/1:100,79,0:99

26 ^CHROM ^POS ^{ID REF ALT}

U00096 470149 . G C

C missense_variant MODERATE mdlA b0448 transcript AAC73551.1 Coding 1/1 c.1279G>C p.Ala427Pro 1279/1773 1279/1773 427/590 U00096 gene 468871-

470643

+ mdlA b0448 mdl EcoGene:EG11622

U00096 CDS 468871- 470643

+ mdlA b0448 mdl EcoGene:EG11622 GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0042493 - response to drug 1 11 putative multidrug ABC transporter ATPase AAC73551.1

RESULTS_dnaQ

27 ^CHROM ^POS ^{ID REF ALT}

U00096 528614 . T A

A missense_variant MODERATE rhsH b0499 transcript b0499 Coding 1/1 c.663T>A p.His221Gln 663/708 663/708 221/235

A upstream_gene_variant MODIFIER ybbD b0501 transcript b0501 Coding c.-1T>A 26 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS U00096 gene 527952-

528659

+ rhsH b0499 ylbH EcoGene:EG14327

U00096 CDS 527952- 528659

+ rhsH b0499 ylbH EcoGene:EG14327 pseudogene, Rhs family C-terminal fragment with unique putative toxin domain 1 11

RESULTS_dnaQ

RESULTS_CIQ4J 4.13 . 13 -2.269933e+00 0.4998 1 6,5,0,2 60 6.2 0.46,1,1,0.0057 5.960000e-02 GT:PL:GQ 0/1:32,0,247:31

28 ^CHROM ^POS ^ID ^REF ^ALT

U00096 528614 . TAAAAAAA TAAAAAAAA,TAAAAAAAAA

A frameshift_variant HIGH rhsH b0499 transcript b0499 Coding 1/1 c.670dupA p.Thr224fs 671/708 671/708 224/235 AA frameshift_variant HIGH rhsH b0499 transcript b0499 Coding 1/1 c.669_670dupAA p.Thr224fs 671/708 671/708 224/235

A upstream_gene_variant MODIFIER ybbD b0501 transcript b0501 Coding c.-1dupA 18 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS AA upstream_gene_variant MODIFIER ybbD b0501 transcript b0501 Coding c.-1_-1dupAA 18 WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS

U00096 gene 527952- 528659

+ rhsH b0499 ylbH EcoGene:EG14327

U00096 CDS 527952- 528659

+ rhsH b0499 ylbH EcoGene:EG14327 pseudogene, Rhs family C-terminal fragment with unique putative toxin domain 1 11

RESULTS_dnaQ

RESULTS_CIQ4J 48.5 . 13 1 2 0,0,5,6 60 -64.5 1.075878e-01 10,0.769231 GT:PL:GQ 1/1:89,30,0,73,4,70:57

29 ^CHROM ^POS ^ID ^REF ^ALT

U00096 549551 . CGGG CGG

frameshift_variant HIGH ylbE b4572 transcript ABD18638.2 Coding 1/1 c.1198delG p.Ala400fs 1198/1260 1198/1260 400/419

upstream_gene_variant MODIFIER ylbF b0520 transcript AAC73622.1 Coding c.-1delG 73

U00096 gene 548357-549616 + ylbE b4572 JW0508 EcoGene:EG13398

U00096 CDS 548357-549616 + ylbE b4572 JW0508 EcoGene:EG13398 1 11 NO-induced DUF1116 protein ABD18638.2

RESULTS_dnaQ

(7)

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

U00096 559579 . ACCC ACC

frameshift_variant HIGH sfmC b0531 transcript AAC73633.1 Coding 1/1 c.609delC p.Pro203fs 609/693 609/693 203/230

upstream_gene_variant MODIFIER sfmD b0532 transcript AAC73634.1 Coding c.-1delC 115

U00096 gene 558974- 559666

+ sfmC b0531 JW0520 EcoGene:EG13882

U00096 CDS 558974- 559666

+ sfmC b0531 JW0520 EcoGene:EG13882 putative factor; Surface structures putative chaperone; GO_process:

GO:0006457 - protein folding 1 11 putative periplasmic pilus chaperone AAC73633.1

RESULTS_dnaQ

RESULTS_CIQ4J 45.5 . 20 0.5 1 8,6,1,4 60 48.5 0.3,0.041,1,0.42 1.891781e-01 5,0.250000 GT:PL:GQ 0/1:83,0,231:86

31 ^CHROM ^POS ^ID ^REF ^ALT

U00096 560286 . ATTTTTTT ATTTTTT

frameshift_variant HIGH sfmD b0532 transcript AAC73634.1 Coding 1/1 c.597delT p.Phe199fs 597/2604 597/2604 199/867 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

32 ^CHROM ^POS ^ID ^REF ^ALT

U00096 561965 . GAAAAAAA GAAAAAAAA,GAAAAAAAAA

A frameshift_variant HIGH sfmD b0532 transcript AAC73634.1 Coding 1/1 c.2276dupA p.Asn759fs 2277/2604 2277/2604 759/867 AA frameshift_variant HIGH sfmD b0532 transcript AAC73634.1 Coding 1/1 c.2275_2276dupAA p.Asn759fs 2277/2604 2277/2604 759/867

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

RESULTS_CIQ4J 78.5 . 35 1 2 0,0,20,13 60 -131 1.705934e-01 29,0.828571 GT:PL:GQ 1/1:119,96,0,108,70,105:99

33 ^CHROM ^POS ^{ID REF ALT}

U00096 575625 . A C

C missense_variant MODERATE insH1 b0552 transcript AAC73653.1 Coding 1/1 c.129T>G p.Ile43Met 129/1017 129/1017 43/338

C intron_variant MODIFIER nmpC b0553 transcript b0553 Coding 1/1 c.1040+161T>G

U00096 gene 574737- 575753

- insH1 b0552 ECK0261 EcoGene:EG40008

U00096 CDS 574737- 575753

- insH1 b0552 ECK0261 EcoGene:EG40008 IS, phage, Tn; Transposon-related functions; extrachromosomal; transposon related 1 11 IS5 transposase and trans-activator AAC73653.1

RESULTS_dnaQ

RESULTS_CIQ4J 87.8 . 35 -1.473542e+00 1 2 2,14,15,4 19 -33 0.00013,0.25,1,0.17 1.606673e-01 GT:PL:GQ 1/1:119,6,0:10

34 ^CHROM ^POS ^{ID REF ALT}

U00096 578489 . T C

C missense_variant MODERATE rzpD b0556 transcript AAC73657.1 Coding 1/1 c.383T>C p.Phe128Ser 383/462 383/462 128/153 C missense_variant MODERATE rzoD b4510 transcript ABD18640.1 Coding 1/1 c.163T>C p.Ser55Pro 163/183 163/183 55/60

C downstream_gene_variant MODIFIER borD b0557 transcript AAC73658.1 Coding c.*294A>G 111

U00096 gene 578107- 578568

+ rzpD b0556 ybcT EcoGene:EG13636

U00096 CDS 578107- 578568

+ rzpD b0556 ybcT EcoGene:EG13636 Phage or Prophage Related bacteriophage lambda endopeptidase homolog;

completely contained in another CDS 1 11 DLP12 prophage; putative murein endopeptidase AAC73657.1

(8)

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

35 ^CHROM ^POS ^ID ^REF ^ALT

U00096 584255 . CAAAAAAA CAAAAAA

frameshift_variant HIGH appY b0564 transcript AAC73665.1 Coding 1/1 c.582delA p.Lys194fs 582/750 582/750 194/249 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_process: GO:0006350 - transcription; GO_process: GO:0042594 - response to starvation 1 11 global transcriptional activator; DLP12 prophage AAC73665.1

RESULTS_dnaQ

36 ^CHROM ^POS ^{ID REF ALT}

U00096 595846 . A G

G missense_variant MODERATE cusC b0572 transcript AAC73673.1 Coding 1/1 c.247A>G p.Lys83Glu 247/1374 247/1374 83/457 U00096 gene 595600-

596973

+ cusC b0572 ylcB EcoGene:EG14233

U00096 CDS 595600- 596973

+ cusC b0572 ylcB EcoGene:EG14233 putative transport; Drug/analog sensitivity GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 copper/silver efflux system, outer membrane component AAC73673.1

RESULTS_dnaQ

37 ^CHROM ^POS ^{ID REF ALT}

U00096 598242 . C T

T missense_variant MODERATE cusB b0574 transcript AAC73675.1 Coding 1/1 c.764C>T p.Ala255Val 764/1224 764/1224 255/407 U00096 gene 597479-

598702

+ cusB b0574 ylcD EcoGene:EG14235

U00096 CDS 597479- 598702

+ cusB b0574 ylcD EcoGene:EG14235 putative transport; Drug/analog sensitivity GO_process: GO:0042493 - response to drug 1 11 copper/silver efflux system, membrane fusion protein AAC73675.1

RESULTS_dnaQ

38 ^CHROM ^POS ^{ID REF ALT}

U00096 612097 . G A

A missense_variant MODERATE fepA b0584 transcript AAC73685.1 Coding 1/1 c.398C>T p.Thr133Ile 398/2241 398/2241 133/746 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

RESULTS_dnaQ

39 ^CHROM ^POS ^{ID REF ALT}

U00096 612807 . A G

G missense_variant MODERATE fes b0585 transcript AAC73686.2 Coding 1/1 c.71A>G p.Asn24Ser 71/1203 71/1203 24/400 U00096 gene 612737-

613939

+ fes b0585 JW0576 EcoGene:EG10299

(9)

U00096 CDS 612737- 613939

+ fes b0585 JW0576 EcoGene:EG10299 enzyme; Transport of small molecules: Cations enterochelin esterase;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006826 - iron ion transport 1 11 enterobactin/ferrienterobactin esterase AAC73686.2

RESULTS_dnaQ

RESULTS_CIQ4J 222.0 . 28 0.000000e+00 1 2 1,0,19,8 60 -73 1,0.38,1,0.17 1.680292e-01 GT:PL:GQ 1/1:255,46,0:89

40 ^CHROM ^POS ^ID ^REF ^ALT

U00096 638562 . CTTTTTT CTTTTTTT

T frameshift_variant HIGH dsbG b0604 transcript AAC73705.2 Coding 1/1 c.5_6insA p.Lys3fs 5/747 5/747 2/248

U00096 gene 637827- 638573

- dsbG b0604 ybdP EcoGene:EG13535

U00096 CDS 637827- 638573

- dsbG b0604 ybdP EcoGene:EG13535 enzyme; Central intermediary metabolism: Pool, multipurpose conversions thiol:disulfide interchange protein; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006457 - protein folding 1 11 thiol:disulfide interchange protein, periplasmic AAC73705.2 5.3.4.1

RESULTS_dnaQ

41 ^CHROM ^POS ^{ID REF ALT}

U00096 649456 . T C

C missense_variant MODERATE citF b0615 transcript AAC73716.1 Coding 1/1 c.116A>G p.Glu39Gly 116/1533 116/1533 39/510

C downstream_gene_variant MODIFIER citE b0616 transcript AAC73717.2 Coding c.*909A>G 126

U00096 gene 648039- 649571

- citF b0615 ybdV EcoGene:EG13541

U00096 CDS 648039- 649571

- citF b0615 ybdV EcoGene:EG13541 enzyme; Central intermediary metabolism: Pool, multipurpose conversions citrate lyase alpha chain; GO_component: GO:0005737 - cytoplasm 1 11 citrate lyase, citrate-ACP transferase (alpha) subunit AAC73716.1 4.1.3.6

RESULTS_dnaQ

42 ^CHROM ^POS ^ID ^REF ^ALT

U00096 652353 . ATTTT ATTT

frameshift_variant HIGH citA b0619 transcript AAC73720.1 Coding 1/1 c.123delT p.Phe41fs 123/1659 123/1659 41/552 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

43 ^CHROM ^POS ^{ID REF ALT}

U00096 662009 . G T

T missense_variant MODERATE lipB b0630 transcript AAC73731.2 Coding 1/1 c.270C>A p.Asn90Lys 270/642 270/642 90/213 U00096 gene 661637-

662278

- lipB b0630 JW5089 EcoGene:EG11591

U00096 CDS 661637- 662278

- lipB b0630 JW5089 EcoGene:EG11591 enzyme; Biosynthesis of cofactors, carriers: Lipoate protein of lipoate biosynthesis;

GO_process: GO:0009107 - lipoate biosynthetic process 1 11 octanoyltransferase; octanoyl-[ACP]:protein N- octanoyltransferase AAC73731.2 2.3.1.-

RESULTS_dnaQ

44 ^CHROM ^POS ^{ID REF ALT}

U00096 680675 . C A

(10)

A missense_variant MODERATE djlC b0649 transcript AAC73750.1 Coding 1/1 c.464C>A p.Ala155Asp 464/1452 464/1452 155/483 U00096 gene 680212-

681663

+ djlC b0649 ybeV EcoGene:EG13652

U00096 CDS 680212- 681663

+ djlC b0649 ybeV EcoGene:EG13652 factor; Chaperones 1 11 J domain-containing HscC co-chaperone; Hsc56 AAC73750.1

RESULTS_dnaQ

45 ^CHROM ^POS ^ID ^REF ^ALT

U00096 681550 . GAAAAAAA GAAAAAA

frameshift_variant HIGH djlC b0649 transcript AAC73750.1 Coding 1/1 c.1346delA p.Asn449fs 1346/1452 1346/1452 449/483

downstream_gene_variant MODIFIER hscC b0650 transcript AAC73751.1 Coding c.*1671delT 166

U00096 gene 680212- 681663

+ djlC b0649 ybeV EcoGene:EG13652

U00096 CDS 680212- 681663

+ djlC b0649 ybeV EcoGene:EG13652 factor; Chaperones 1 11 J domain-containing HscC co-chaperone; Hsc56 AAC73750.1

RESULTS_dnaQ

46 ^CHROM ^POS ^{ID REF ALT}

U00096 696211 . T G

G missense_variant MODERATE ubiF b0662 transcript AAC73763.1 Coding 1/1 c.1111T>G p.Leu371Val 1111/1176 1111/1176 371/391 U00096 gene 695101-

696276

+ ubiF b0662 yleB EcoGene:EG13658

U00096 CDS 695101- 696276

+ ubiF b0662 yleB EcoGene:EG13658 1 11 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol oxygenase AAC73763.1 1.14.13.-

RESULTS_dnaQ

47 ^CHROM ^POS ^{ID REF ALT}

U00096 724054 . G A

A missense_variant MODERATE kdpD b0695 transcript AAC73789.1 Coding 1/1 c.361C>T p.His121Tyr 361/2685 361/2685 121/894 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

48 ^CHROM ^POS ^{ID REF ALT}

U00096 737651 . A G

G missense_variant MODERATE ybfL b0705 transcript b0705 Coding 1/1 c.827A>G p.Glu276Gly 827/1137 827/1137 276/378 U00096 gene 736825-

737961

+ ybfL b0705 JW0695 EcoGene:EG13417

U00096 CDS 736825- 737961

+ ybfL b0705 JW0695 EcoGene:EG13417 pseudogene, DDE domain transposase family;putative factor; Not classified;

putative receptor protein 1 11

RESULTS_dnaQ

RESULTS_CIQ4J 222.0 . 20 6.936880e-01 1 2 0,1,9,10 56 -49 1,0.35,0.45,0.15 5.293301e-02 GT:PL:GQ 1/1:255,22,0:41

49 ^CHROM ^POS ^{ID REF ALT}

U00096 744025 . C T

(11)

T stop_gained HIGH ybgJ b0711 transcript AAC73805.1 Coding 1/1 c.433C>T p.Gln145* 433/657 433/657 145/218 U00096 gene 743593-

744249

+ ybgJ b0711 JW0701 EcoGene:EG13306

U00096 CDS 743593- 744249

+ ybgJ b0711 JW0701 EcoGene:EG13306 putative enzyme; Not classified putative carboxylase 1 11 putative allophanate hydrolase, subunit 1 AAC73805.1

RESULTS_dnaQ

50 ^CHROM ^POS ^{ID REF ALT}

U00096 749521 . C T

T missense_variant MODERATE ybgP b0717 transcript AAC73811.1 Coding 1/1 c.187G>A p.Glu63Lys 187/729 187/729 63/242 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

51 ^CHROM ^POS ^{ID REF ALT}

U00096 771585 . C T

T missense_variant MODERATE cydA b0733 transcript AAC73827.2 Coding 1/1 c.128C>T p.Ser43Phe 128/1569 128/1569 43/522 U00096 gene 771458-

773026

+ cydA b0733 JW0722 EcoGene:EG10173

U00096 CDS 771458- 773026

+ cydA b0733 JW0722 EcoGene:EG10173 enzyme; Energy metabolism, carbon: Electron transport cytochrome d terminal oxidase, polypeptide subunit I; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane 1 11 cytochrome d terminal oxidase, subunit I AAC73827.2 1.9.3.- N-terminus verified by Edman degradation: PMID 10428033

RESULTS_dnaQ

52 ^CHROM ^POS ^{ID REF ALT}

U00096 792039 . G A

A missense_variant MODERATE galE b0759 transcript AAC73846.1 Coding 1/1 c.17C>T p.Thr6Ile 17/1017 17/1017 6/338 U00096 gene 791039-

792055

- galE b0759 JW0742 EcoGene:EG10362

U00096 CDS 791039- 792055

- galE b0759 JW0742 EcoGene:EG10362 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_function: GO:0042280 - cell surface antigen activity, host-interacting; GO_process:

GO:0006012 - galactose metabolic process; GO_process: GO:0009242 - colanic acid biosynthetic process; GO_process:

GO:0016052 - carbohydrate catabolic process; GO_process: GO:0009435 - NAD biosynthetic process; GO_process:

GO:0009269 - response to desiccation 1 11 UDP-galactose-4-epimerase AAC73846.1 5.1.3.2 N-terminus verified by Edman degradation: PMID 4613352,9119048

RESULTS_dnaQ

53 ^CHROM ^POS ^{ID REF ALT}

U00096 800479 . C T

T missense_variant MODERATE ybhD b0768 transcript AAC73855.2 Coding 1/1 c.97G>A p.Ala33Thr 97/954 97/954 33/317 U00096 gene 799622-

800575

- ybhD b0768 JW5896 EcoGene:EG13230

U00096 CDS 799622- 800575

- ybhD b0768 JW5896 EcoGene:EG13230 putative regulator; Not classified putative transcriptional regulator LYSR-type;

GO_process: GO:0006350 - transcription 1 11 putative DNA-binding transcriptional regulator AAC73855.2

RESULTS_dnaQ

RESULTS_CIQ4J 37.0 . 14 6.227992e-01 0.5 1 3,8,1,2 60 40 1,1,1,1 6.186179e-02 GT:PL:GQ 0/1:67,0,227:70

(12)

54 U00096 836709 . ^CHROM ^POS ^{ID REF ALT} A C

C missense_variant MODERATE ybiC b0801 transcript AAC73888.1 Coding 1/1 c.359A>C p.His120Pro 359/1086 359/1086 120/361 U00096 gene 836351-

837436

+ ybiC b0801 JW0786 EcoGene:EG11581

U00096 CDS 836351- 837436

+ ybiC b0801 JW0786 EcoGene:EG11581 putative enzyme; Not classified 1 11 putative dehydrogenase AAC73888.1

RESULTS_dnaQ

55 ^CHROM ^POS ^ID ^REF ^ALT

U00096 856126 . TGGG TGG

frameshift_variant HIGH ybiT b0820 transcript AAC73907.1 Coding 1/1 c.167delG p.Gly56fs 167/1593 167/1593 56/530 U00096 gene 855963-

857555

+ ybiT b0820 JW0804 EcoGene:EG13325

U00096 CDS 855963- 857555

+ ybiT b0820 JW0804 EcoGene:EG13325 putative factor; Not classified putative ATP-binding component of a transport system; GO_component: GO:0005737 - cytoplasm 1 11 ABC-F family putative regulatory ATPase AAC73907.1

RESULTS_dnaQ

56 ^CHROM ^POS ^{ID REF ALT}

U00096 881801 . A G

G missense_variant MODERATE dacC b0839 transcript AAC73926.1 Coding 1/1 c.1075A>G p.Asn359Asp 1075/1203 1075/1203 359/400

G downstream_gene_variant MODIFIER deoR b0840 transcript AAC73927.1 Coding c.*759T>C 175

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

57 ^CHROM ^POS ^{ID REF ALT}

U00096 897586 . G A

A missense_variant MODERATE potI b0857 transcript AAC73944.1 Coding 1/1 c.503G>A p.Arg168His 503/846 503/846 168/281 U00096 gene 897084-

897929

+ potI b0857 JW0841 EcoGene:EG11632

U00096 CDS 897084- 897929

+ potI b0857 JW0841 EcoGene:EG11632 transport; Transport of small molecules: Amino acids, amines putrescine transport protein; permease; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0006596 - polyamine biosynthetic process; GO_process: GO:0009310 - amine catabolic process; GO_process: GO:0015847 - putrescine transport 1 11 putrescine ABC transporter permease AAC73944.1

RESULTS_dnaQ

58 ^CHROM ^POS ^ID ^REF ^ALT

U00096 916501 . GTTTT GTTT

frameshift_variant HIGH ybjD b0876 transcript AAC73963.1 Coding 1/1 c.33delT p.Phe11fs 33/1659 33/1659 11/552 U00096 gene 916473-

918131

+ ybjD b0876 JW0860 EcoGene:EG13425

U00096 CDS 916473- 918131

+ ybjD b0876 JW0860 EcoGene:EG13425 1 11 putative OLD family ATP-dependent endonuclease; DUF2813 family protein AAC73963.1

RESULTS_dnaQ

(13)

59 ^CHROM ^POS ^{ID REF ALT}

U00096 925507 . T A

A missense_variant MODERATE clpA b0882 transcript AAC73969.1 Coding 1/1 c.2244T>A p.Ser748Arg 2244/2277 2244/2277 748/758 U00096 gene 923264-

925540

+ clpA b0882 lopD EcoGene:EG10156

U00096 CDS 923264- 925540

+ clpA b0882 lopD EcoGene:EG10156 enzyme; Degradation of proteins, peptides, glyco ATP-binding component of serine protease; GO_component: GO:0005737 - cytoplasm 1 11 ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity AAC73969.1 N-terminus verified by Edman degradation: PMID 3049606

RESULTS_dnaQ

60 ^CHROM ^POS ^{ID REF ALT}

U00096 974815 . A G

G missense_variant MODERATE mukF b0922 transcript AAC74008.1 Coding 1/1 c.497A>G p.Glu166Gly 497/1323 497/1323 166/440 U00096 gene 974319-

975641

+ mukF b0922 kicB EcoGene:EG12165

U00096 CDS 974319- 975641

+ mukF b0922 kicB EcoGene:EG12165 factor; Cell killing mukF protein (killing factor KICB) 1 11 chromosome condensin MukBEF, kleisin-like subunit, binds calcium AAC74008.1

RESULTS_dnaQ

61 ^CHROM ^POS ^{ID REF ALT}

U00096 982175 . A G

G missense_variant MODERATE ldtD b0925 transcript AAC74011.1 Coding 1/1 c.1129A>G p.Ile377Val 1129/1848 1129/1848 377/615 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

62 ^CHROM ^POS ^ID ^REF ^ALT

U00096 989477 . CTTTTT CTTTT

frameshift_variant HIGH pncB b0931 transcript AAC74017.1 Coding 1/1 c.875delA p.Glu292fs 875/1203 875/1203 292/400 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

63 ^CHROM ^POS ^{ID REF ALT}

U00096 991998 . G T

T missense_variant MODERATE pepN b0932 transcript AAC74018.1 Coding 1/1 c.1377G>T p.Glu459Asp 1377/2613 1377/2613 459/870 U00096 gene 990622-

993234

+ pepN b0932 JW0915 EcoGene:EG10696

U00096 CDS 990622- 993234

+ pepN b0932 JW0915 EcoGene:EG10696 enzyme; Degradation of proteins, peptides, glyco 1 11 aminopeptidase N AAC74018.1 3.4.11.2 N-terminus verified by Edman degradation: PMID 2869947

RESULTS_dnaQ

(14)

64 U00096 1037262 . ^CHROM ^POS ^{ID REF ALT} C T

T missense_variant MODERATE hyaF b0977 transcript AAC74062.1 Coding 1/1 c.514C>T p.His172Tyr 514/858 514/858 172/285 U00096 gene 1036749-

1037606

+ hyaF b0977 JW0959 EcoGene:EG10473

U00096 CDS 1036749- 1037606

+ hyaF b0977 JW0959 EcoGene:EG10473 phenotype; Energy metabolism, carbon: Aerobic respiration nickel incorporation into hydrogenase-1 proteins; GO_process: GO:0009060 - aerobic respiration; GO_process: GO:0009061 - anaerobic respiration; GO_process: GO:0006457 - protein folding 1 11 hydrogenase-1 protein nickel incorporation factor AAC74062.1

RESULTS_dnaQ

65 ^CHROM ^POS ^{ID REF ALT}

U00096 1047912 . C A

A missense_variant MODERATE gfcD b0984 transcript AAC74069.1 Coding 1/1 c.34G>T p.Ala12Ser 34/2097 34/2097 12/698

A downstream_gene_variant MODIFIER gfcC b0985 transcript AAC74070.1 Coding c.*747G>T 33

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

66 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1048804 . GTTTTT GTTTT

frameshift_variant HIGH gfcB b0986 transcript AAC74071.1 Coding 1/1 c.524delA p.Glu175fs 524/645 524/645 175/214

upstream_gene_variant MODIFIER gfcC b0985 transcript AAC74070.1 Coding c.-1delA 118

U00096 gene 1048688- 1049332

- gfcB b0986 ymcC EcoGene:EG13731

U00096 CDS 1048688- 1049332

- gfcB b0986 ymcC EcoGene:EG13731 putative regulator; Not classified putative regulator 1 11 O-antigen capsule production lipoprotein AAC74071.1

RESULTS_dnaQ

67 ^CHROM ^POS ^{ID REF ALT}

U00096 1065842 . G T

T missense_variant MODERATE agp b1002 transcript AAC74087.1 Coding 1/1 c.258G>T p.Met86Ile 258/1242 258/1242 86/413 U00096 gene 1065585-

1066826

+ agp b1002 JW0987 EcoGene:EG10033

U00096 CDS 1065585- 1066826

+ agp b1002 JW0987 EcoGene:EG10033 enzyme; Central intermediary metabolism: Pool, multipurpose conversions periplasmic glucose-1-phosphatase; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006006 - glucose metabolic process 1 11 glucose-1-phosphatase/inositol phosphatase AAC74087.1 3.1.3.10

RESULTS_dnaQ

68 ^CHROM ^POS ^{ID REF ALT}

U00096 1069550 . G A

A missense_variant MODERATE rutG b1006 transcript AAC74091.2 Coding 1/1 c.290C>T p.Ala97Val 290/1329 290/1329 97/442 U00096 gene 1068511-

1069839

- rutG b1006 ycdG EcoGene:EG13853

U00096 CDS 1068511- 1069839

- rutG b1006 ycdG EcoGene:EG13853 transport; Pyrimidine nitrogen catabolism putative transport protein;

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 pyrimidine permease AAC74091.2

RESULTS_dnaQ

(15)

69 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1107726 . CGGG CGG

frameshift_variant HIGH clsC b1046 transcript AAC74130.2 Coding 1/1 c.1375delG p.Val459fs 1375/1422 1375/1422 459/473

downstream_gene_variant MODIFIER opgC b1047 transcript AAC74131.1 Coding c.*1158delC 55

U00096 gene 1106355- 1107776

+ clsC b1046 ymdC EcoGene:EG13875

U00096 CDS 1106355- 1107776

+ clsC b1046 ymdC EcoGene:EG13875 Enzyme; Macromolecule synthesis: Phospholipids putative synthase 1 11 stationary phase cardiolipin synthase 3 AAC74130.2

RESULTS_dnaQ

70 ^CHROM ^POS ^{ID REF ALT}

U00096 1125850 . G A

A missense_variant MODERATE rimJ b1066 transcript AAC74150.1 Coding 1/1 c.289G>A p.Val97Ile 289/585 289/585 97/194 U00096 gene 1125562-

1126146

+ rimJ b1066 tcp EcoGene:EG10851

U00096 CDS 1125562- 1126146

+ rimJ b1066 tcp EcoGene:EG10851 enzyme; Ribosomes - maturation and modification acetylation of N-terminal alanine of 30S ribosomal subunit protein S5; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006464 - protein modification process 1 11 ribosomal-protein-S5-alanine N-acetyltransferase AAC74150.1 2.3.1.128

RESULTS_dnaQ

71 ^CHROM ^POS ^{ID REF ALT}

U00096 1147182 . C T

T missense_variant MODERATE yceD b1088 transcript AAC74172.1 Coding 1/1 c.389C>T p.Ala130Val 389/522 389/522 130/173

T upstream_gene_variant MODIFIER rpmF b1089 transcript AAC74173.1 Coding c.-1C>T 185

U00096 gene 1146794-1147315 + yceD b1088 JW1074 EcoGene:EG11119

U00096 CDS 1146794-1147315 + yceD b1088 JW1074 EcoGene:EG11119 1 11 DUF177 family protein AAC74172.1

RESULTS_dnaQ

72 ^CHROM ^POS ^{ID REF ALT}

U00096 1177323 . G A

A missense_variant MODERATE lolE b1118 transcript AAC74202.1 Coding 1/1 c.4G>A p.Ala2Thr 4/1245 4/1245 2/414

A downstream_gene_variant MODIFIER lolD b1117 transcript AAC74201.2 Coding c.*702G>A 3

U00096 gene 1177320- 1178564

+ lolE b1118 ycfW EcoGene:EG13441

U00096 CDS 1177320- 1178564

+ lolE b1118 ycfW EcoGene:EG13441 putative enzyme; Not classified putative kinase; membrane component of ABC superfamily; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 lipoprotein-releasing system transmembrane protein AAC74202.1

RESULTS_dnaQ

73 ^CHROM ^POS ^{ID REF ALT}

U00096 1180733 . C G

G missense_variant MODERATE ycfZ b1121 transcript AAC74205.1 Coding 1/1 c.535G>C p.Gly179Arg 535/789 535/789 179/262

U00096 gene 1180479-1181267 - ycfZ b1121 JW1107 EcoGene:EG13444

U00096 CDS 1180479-1181267 - ycfZ b1121 JW1107 EcoGene:EG13444 putative factor; Not classified 1 11 inner membrane protein AAC74205.1

RESULTS_dnaQ

RESULTS_CIQ4J 3.01 . 15 -2.282177e+00 0.4997 1 5,7,1,1 60 4.77 1,0.069,1,0.019 7.840000e-02 GT:PL:GQ 0/1:30,0,255:28

(16)

74 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1180733 . CGGGGGG CGGGGGGG

G frameshift_variant HIGH ycfZ b1121 transcript AAC74205.1 Coding 1/1 c.528_529insC p.Pro177fs 528/789 528/789 176/262 U00096 gene 1180479-1181267 - ycfZ b1121 JW1107 EcoGene:EG13444

U00096 CDS 1180479-1181267 - ycfZ b1121 JW1107 EcoGene:EG13444 putative factor; Not classified 1 11 inner membrane protein AAC74205.1

RESULTS_dnaQ

RESULTS_CIQ4J 76.5 . 15 1 2 1,0,5,7 60 -56.5 0.46,1,1,0.13 1.254183e-01 9,0.600000 GT:PL:GQ 1/1:117,22,0:41

75 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1184872 . GTTTTT GTTTT

frameshift_variant HIGH potA b1126 transcript AAC74210.1 Coding 1/1 c.718delA p.Lys240fs 718/1137 718/1137 240/378 U00096 gene 1184458-

1185594

- potA b1126 JW1112 EcoGene:EG10749

U00096 CDS 1184458- 1185594

- potA b1126 JW1112 EcoGene:EG10749 transport; Transport of small molecules: Amino acids, amines ATP-binding component of spermidine/putrescine transport; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006596 - polyamine biosynthetic process; GO_process: GO:0009310 - amine catabolic process 1 11 spermidine/putrescine ABC transporter ATPase AAC74210.1

RESULTS_dnaQ

76 ^CHROM ^POS ^{ID REF ALT}

U00096 1199190 . G A

A missense_variant MODERATE lit b1139 transcript AAC74223.1 Coding 1/1 c.496G>A p.Val166Ile 496/894 496/894 166/297 U00096 gene 1198695-

1199588

+ lit b1139 JW1125 EcoGene:EG10535

U00096 CDS 1198695- 1199588

+ lit b1139 JW1125 EcoGene:EG10535 membrane; Phage or Prophage Related phage T4 late gene expression; at locus of e14 element 1 11 T4 phage exclusion protein; cell death peptidase, e14 prophage AAC74223.1

RESULTS_dnaQ

77 ^CHROM ^POS ^{ID REF ALT}

U00096 1203691 . ATTT ATT

frameshift_variant HIGH ymfL b1147 transcript AAC74231.2 Coding 1/1 c.427delT p.Ser143fs 427/558 427/558 143/185

upstream_gene_variant MODIFIER ymfM b1148 transcript AAC74232.1 Coding c.-1delT 128

U00096 gene 1203268- 1203825

+ ymfL b1147 JW1133 EcoGene:EG14250

U00096 CDS 1203268- 1203825

+ ymfL b1147 JW1133 EcoGene:EG14250 Phage or Prophage Related 1 11 e14 prophage; putative DNA-binding transcriptional regulator AAC74231.2

RESULTS_dnaQ

78 ^CHROM ^POS ^{ID REF ALT}

U00096 1203692 . T A

A missense_variant MODERATE ymfL b1147 transcript AAC74231.2 Coding 1/1 c.425T>A p.Ile142Asn 425/558 425/558 142/185

A upstream_gene_variant MODIFIER ymfM b1148 transcript AAC74232.1 Coding c.-1T>A 130

U00096 gene 1203268- 1203825

+ ymfL b1147 JW1133 EcoGene:EG14250

U00096 CDS 1203268- 1203825

+ ymfL b1147 JW1133 EcoGene:EG14250 Phage or Prophage Related 1 11 e14 prophage; putative DNA-binding transcriptional regulator AAC74231.2

RESULTS_dnaQ

Non synonimous mutations found in sample: CIQ4J