Non synonimous mutations found in sample: CIM5H

(1)

Non synonimous mutations found in sample: CIM5H

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 89890 . T A

A missense_variant MODERATE mraZ b0081 transcript AAC73192.1 Coding 1/1 c.257T>A p.Met86Lys 257/459 257/459 86/152

U00096 gene 89634-90092 + mraZ b0081 yabB EcoGene:EG11084

U00096 CDS 89634-90092 + mraZ b0081 yabB EcoGene:EG11084 1 11 RsmH methytransferase inhibitor AAC73192.1

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

RESULTS_MG1655

RESULTS_CIM5H 222.0 . 41 1 2 0,0,15,26 60 -150 3.313144e-01 GT:PL:GQ 1/1:255,123,0:99

2 CHROM POS ID REF ALT U00096 94873 . T A

A missense_variant MODERATE murF b0086 transcript AAC73197.1 Coding 1/1 c.224T>A p.Leu75Gln 224/1359 224/1359 75/452 U00096 gene 94650-

96008

+ murF b0086 mra EcoGene:EG10622

U00096 CDS 94650- 96008

+ murF b0086 mra EcoGene:EG10622 enzyme; Murein sacculus, peptidoglycan GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009252 - peptidoglycan biosynthetic process; GO_process: GO:0000270 - peptidoglycan metabolic process 1 11 UDP-N-acetylmuramoyl- tripeptide:D-alanyl-D- alanine ligase AAC73197.1 6.3.2.10 N-terminus verified by Edman degradation: PMID 2186811

RESULTS_MG1655

3 ^CHROM ^POS ^{ID REF ALT}

U00096 134658 . A G

G missense_variant MODERATE yacL b0119 transcript AAC73230.2 Coding 1/1 c.271A>G p.Asn91Asp 271/363 271/363 91/120

G downstream_gene_variant MODIFIER speD b0120 transcript AAC73231.1 Coding c.*795T>C 130

U00096 gene 134388-134750 + yacL b0119 JW0115 EcoGene:EG12605

U00096 CDS 134388-134750 + yacL b0119 JW0115 EcoGene:EG12605 1 11 UPF0231 family protein AAC73230.2

RESULTS_MG1655

4 ^CHROM ^POS ^{ID REF ALT}

U00096 153617 . T C

C missense_variant MODERATE htrE b0139 transcript AAC73250.1 Coding 1/1 c.1810A>G p.Ser604Gly 1810/2598 1810/2598 604/865 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_MG1655

5 ^CHROM ^POS ^{ID REF ALT}

U00096 157376 . C T

T missense_variant MODERATE folK b0142 transcript AAC73253.1 Coding 1/1 c.357G>A p.Met119Ile 357/480 357/480 119/159 U00096 gene 157253-

157732

- folK b0142 JW0138 EcoGene:EG11374

U00096 CDS 157253- 157732

- folK b0142 JW0138 EcoGene:EG11374 enzyme; Biosynthesis of cofactors, carriers: Folic acid 7,8-dihydro-6- hydroxymethylpterin- pyrophosphokinase; GO_process: GO:0046656 - folic acid biosynthetic process 1 11 2-amino-4- hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase AAC73253.1 2.7.6.3

(2)

RESULTS_MG1655

6 ^CHROM ^POS ^{ID REF ALT}

U00096 168654 . GA G

frameshift_variant HIGH fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172delA p.Asp391fs 1172/2244 1172/2244 391/747 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_MG1655

RESULTS_CIM5H 214.0 . 32 1 2 0,0,13,18 60 -128 1.509967e-01 28,0.875000 GT:PL:GQ 1/1:255,93,0:99

7 ^CHROM ^POS ^{ID REF ALT}

U00096 168655 . A G,T

G missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172A>G p.Asp391Gly 1172/2244 1172/2244 391/747 T missense_variant MODERATE fhuA b0150 transcript AAC73261.1 Coding 1/1 c.1172A>T p.Asp391Val 1172/2244 1172/2244 391/747

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_MG1655

RESULTS_CIM5H 90.5 . 5 1 2 0,0,1,4 60 -39 9.843946e-03 GT:PL:GQ 1/1:142,31,19,118,0,115:21

8 ^CHROM ^POS ^{ID REF ALT}

U00096 218480 . C T

T missense_variant MODERATE proS b0194 transcript AAC73305.1 Coding 1/1 c.296G>A p.Arg99His 296/1719 296/1719 99/572 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_MG1655

9 ^CHROM ^POS ^{ID REF ALT}

U00096 233614 . C T

T missense_variant MODERATE mltD b0211 transcript AAC73316.1 Coding 1/1 c.342G>A p.Met114Ile 342/1359 342/1359 114/452 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_MG1655

10 ^CHROM ^POS ^{ID REF ALT}

U00096 236552 . C A

A missense_variant MODERATE dnaQ b0215 transcript AAC73320.1 Coding 1/1 c.486C>A p.His162Gln 486/732 486/732 162/243 U00096 gene 236067-

236798

+ dnaQ b0215 mutD EcoGene:EG10243

(3)

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_MG1655

11 ^CHROM ^POS ^{ID REF ALT}

U00096 245180 . C A

A missense_variant MODERATE yafK b0224 transcript AAC73328.1 Coding 1/1 c.626G>T p.Arg209Leu 626/741 626/741 209/246

A downstream_gene_variant MODIFIER yafJ b0223 transcript AAC73327.1 Coding c.*768C>A 86

U00096 gene 245065-245805 - yafK b0224 JW0214 EcoGene:EG13148

U00096 CDS 245065-245805 - yafK b0224 JW0214 EcoGene:EG13148 1 11 L,D-transpeptidase-related protein AAC73328.1

RESULTS_MG1655

12 ^CHROM ^POS ^{ID REF ALT}

U00096 294118 . G A

A missense_variant MODERATE yagM b0279 transcript AAC73382.1 Coding 1/1 c.682C>T p.Leu228Phe 682/855 682/855 228/284

A upstream_gene_variant MODIFIER yagL b0278 transcript AAC73381.1 Coding c.-1C>T 200

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_MG1655

13 ^CHROM ^POS ^{ID REF ALT}

U00096 306370 . C T

T missense_variant MODERATE ecpD b0290 transcript AAC73393.1 Coding 1/1 c.448G>A p.Gly150Ser 448/1644 448/1644 150/547 U00096 gene 305174-

306817

- ecpD b0290 yagW EcoGene:EG13562

U00096 CDS 305174- 306817

- ecpD b0290 yagW EcoGene:EG13562 structural component; Surface structures putative receptor 1 11 polymerized tip adhesin of ECP fibers AAC73393.1

RESULTS_MG1655

14 ^CHROM ^POS ^ID ^REF ^ALT

U00096 309214 . ACCCC ACCC

frameshift_variant HIGH ecpC b0291 transcript AAC73394.1 Coding 1/1 c.115delG p.Gly39fs 115/2526 115/2526 39/841

downstream_gene_variant MODIFIER ecpB b0292 transcript AAC73395.1 Coding c.*669delG 140

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_MG1655

15 ^CHROM ^POS ^{ID REF ALT}

U00096 349262 . C T

T missense_variant MODERATE prpB b0331 transcript AAC73434.1 Coding 1/1 c.581C>T p.Ala194Val 581/891 581/891 194/296 U00096 gene 348682-

349572

+ prpB b0331 yahQ EcoGene:EG13601

U00096 CDS 348682- + prpB b0331 yahQ EcoGene:EG13601 putative enzyme; Not classified putative phosphonomutase 2; GO_component:

(4)

349572 GO:0005737 - cytoplasm; GO_process: GO:0019395 - fatty acid oxidation 1 11 2-methylisocitrate lyase AAC73434.1 4.1.3.30

RESULTS_MG1655

16 ^CHROM ^POS ^{ID REF ALT}

U00096 353381 . G A

A missense_variant MODERATE prpE b0335 transcript AAC73438.1 Coding 1/1 c.676G>A p.Val226Met 676/1887 676/1887 226/628 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_MG1655

17 ^CHROM ^POS ^ID ^REF ^ALT

U00096 361721 . CTTTTTT CTTTTTTT

T frameshift_variant HIGH lacA b0342 transcript AAC73445.1 Coding 1/1 c.133_134insA p.Lys46fs 133/612 133/612 45/203

T downstream_gene_variant MODIFIER lacY b0343 transcript AAC73446.1 Coding c.*1254_*1254insA 198

U00096 gene 361249- 361860

- lacA b0342 JW0333 EcoGene:EG10524

U00096 CDS 361249- 361860

- lacA b0342 JW0333 EcoGene:EG10524 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 thiogalactoside acetyltransferase AAC73445.1 2.3.1.18 N-terminus verified by Edman degradation: PMID 3922433

RESULTS_MG1655

RESULTS_CIM5H 95.5 . 17 1 2 0,0,9,6 60 -79.5 1.597455e-01 14,0.823529 GT:PL:GQ 1/1:136,45,0:87

18 ^CHROM ^POS ^{ID REF ALT}

U00096 366168 . A T

T missense_variant MODERATE lacZ b0344 transcript AAC73447.1 Coding 1/1 c.138T>A p.Asp46Glu 138/3075 138/3075 46/1024 U00096 gene 363231-

366305

- lacZ b0344 JW0335 EcoGene:EG10527

U00096 CDS 363231- 366305

- lacZ b0344 JW0335 EcoGene:EG10527 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 beta-D-galactosidase AAC73447.1 3.2.1.23

RESULTS_MG1655

19 ^CHROM ^POS ^{ID REF ALT}

U00096 397213 . A T

T missense_variant MODERATE sbmA b0377 transcript AAC73480.1 Coding 1/1 c.575A>T p.Gln192Leu 575/1221 575/1221 192/406 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_MG1655

20 ^CHROM ^POS ^{ID REF ALT}

U00096 402171 . T A

A missense_variant MODERATE phoA b0383 transcript AAC73486.2 Coding 1/1 c.425T>A p.Leu142Gln 425/1416 425/1416 142/471 U00096 gene 401747- + phoA b0383 psiA EcoGene:EG10727

(5)

403162 U00096 CDS 401747-

403162

+ phoA b0383 psiA EcoGene:EG10727 enzyme; Central intermediary metabolism: Phosphorus compounds alkaline phosphatase; start codon corrected; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0006793 - phosphorus metabolic process 1 11 bacterial alkaline phosphatase AAC73486.2 3.1.3.1

RESULTS_MG1655

21 ^CHROM ^POS ^{ID REF ALT}

U00096 435879 . T A

A missense_variant MODERATE thiL b0417 transcript AAC73520.1 Coding 1/1 c.246T>A p.Asp82Glu 246/978 246/978 82/325 U00096 gene 435634-

436611

+ thiL b0417 JW0407 EcoGene:EG20227

U00096 CDS 435634- 436611

+ thiL b0417 JW0407 EcoGene:EG20227 enzyme; Biosynthesis of cofactors, carriers: Thiamine GO_process: GO:0009228 - thiamin biosynthetic process 1 11 thiamine monophosphate kinase AAC73520.1 2.7.4.16

RESULTS_MG1655

22 ^CHROM ^POS ^{ID REF ALT}

U00096 447488 . T C

C missense_variant MODERATE cyoE b0428 transcript AAC73531.1 Coding 1/1 c.218A>G p.Asn73Ser 218/891 218/891 73/296 U00096 gene 446815-

447705

- cyoE b0428 JW0418 EcoGene:EG10182

U00096 CDS 446815- 447705

- cyoE b0428 JW0418 EcoGene:EG10182 enzyme; Energy metabolism, carbon: Aerobic respiration protoheme IX farnesyltransferase (haeme O biosynthesis); GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009060 - aerobic respiration 1 11 protoheme IX farnesyltransferase AAC73531.1 2.5.1.-

RESULTS_MG1655

23 ^CHROM ^POS ^{ID REF ALT}

U00096 448089 . CAAA CAA

frameshift_variant HIGH cyoC b0430 transcript AAC73533.1 Coding 1/1 c.569delT p.Val190fs 569/615 569/615 190/204

upstream_gene_variant MODIFIER cyoD b0429 transcript AAC73532.1 Coding c.-1delT 46

U00096 gene 448046- 448660

- cyoC b0430 JW0420 EcoGene:EG10180

U00096 CDS 448046- 448660

- cyoC b0430 JW0420 EcoGene:EG10180 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 III AAC73533.1 1.10.3.-

RESULTS_MG1655

24 ^CHROM ^POS ^{ID REF ALT}

U00096 453654 . C G

G missense_variant MODERATE yajG b0434 transcript AAC73537.2 Coding 1/1 c.514G>C p.Asp172His 514/579 514/579 172/192

G upstream_gene_variant MODIFIER ampG b0433 transcript AAC73536.1 Coding c.-1G>C 109

U00096 gene 453589- 454167

- yajG b0434 JW0424 EcoGene:EG12182

U00096 CDS 453589- 454167

- yajG b0434 JW0424 EcoGene:EG12182 putative enzyme; Not classified putative polymerase/proteinase 1 11 putative lipoprotein AAC73537.2

RESULTS_MG1655

25 ^CHROM ^POS ^{ID REF ALT}

U00096 475050 . G A

(6)

A stop_gained HIGH tesB b0452 transcript AAC73555.1 Coding 1/1 c.112C>T p.Gln38* 112/861 112/861 38/286 U00096 gene 474301-

475161

- tesB b0452 JW0442 EcoGene:EG10995

U00096 CDS 474301- 475161

- tesB b0452 JW0442 EcoGene:EG10995 enzyme; Fatty acid and phosphatidic acid biosynthesis 1 11 acyl-CoA thioesterase 2 AAC73555.1 3.1.2.-

RESULTS_MG1655

26 ^CHROM ^POS ^{ID REF ALT}

U00096 475469 . C T

T missense_variant MODERATE ybaY b0453 transcript AAC73556.1 Coding 1/1 c.91C>T p.Pro31Ser 91/573 91/573 31/190 U00096 gene 475379-

475951

+ ybaY b0453 JW0443 EcoGene:EG13253

U00096 CDS 475379- 475951

+ ybaY b0453 JW0443 EcoGene:EG13253 phenotype; Not classified glycoprotein/polysaccharide metabolism; GO_process:

GO:0042158 - lipoprotein biosynthetic process; GO_process: GO:0009101 - glycoprotein biosynthetic process 1 11 outer membrane lipoprotein AAC73556.1

RESULTS_MG1655

27 ^CHROM ^POS ^{ID REF ALT}

U00096 511329 . G T

T stop_gained HIGH copA b0484 transcript AAC73586.1 Coding 1/1 c.51C>A p.Cys17* 51/2505 51/2505 17/834

U00096 gene 508875- 511379

- copA b0484 ybaR EcoGene:EG13246

U00096 CDS 508875- 511379

- copA b0484 ybaR EcoGene:EG13246 putative enzyme; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_function: GO:0015662 - ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 1 11 copper transporter AAC73586.1 3.6.3.4

RESULTS_MG1655

RESULTS_CIM5H 222.0 . 38 -6.864065e-01 1 2 1,1,16,20 60 -65 1,0.29,1,0.24 2.900899e-01 GT:PL:GQ 1/1:255,38,0:73

28 ^CHROM ^POS ^{ID REF ALT}

U00096 514719 . C T

T stop_gained HIGH ybbJ b0488 transcript AAC73590.2 Coding 1/1 c.141G>A p.Trp47* 141/459 141/459 47/152

T downstream_gene_variant MODIFIER qmcA b0489 transcript AAC73591.1 Coding c.*918G>A 137

U00096 gene 514401- 514859

- ybbJ b0488 JW5065 EcoGene:EG13257

U00096 CDS 514401- 514859

- ybbJ b0488 JW5065 EcoGene:EG13257 1 11 inner membrane protein; stimulator of the QmcA suppressor of ftsH- htpX AAC73590.2

RESULTS_MG1655

29 ^CHROM ^POS ^{ID REF ALT}

U00096 551066 . G T

T missense_variant MODERATE ybcF b0521 transcript AAC73623.1 Coding 1/1 c.628G>T p.Ala210Ser 628/894 628/894 210/297 U00096 gene 550439-

551332

+ ybcF b0521 JW0510 EcoGene:EG12384

U00096 CDS 550439- 551332

+ ybcF b0521 JW0510 EcoGene:EG12384 putative enzyme; Purine nitrogen catabolism putative carbamate kinase;

GO_process: GO:0006526 - arginine biosynthetic process; GO_process: GO:0006221 - pyrimidine nucleotide biosynthetic process 1 11 putative carbonate kinase AAC73623.1

RESULTS_MG1655

30 ^CHROM ^POS ^{ID REF ALT}

U00096 578636 . A T

(7)

T stop_gained HIGH borD b0557 transcript AAC73658.1 Coding 1/1 c.258T>A p.Tyr86* 258/294 258/294 86/97

T downstream_gene_variant MODIFIER rzpD b0556 transcript AAC73657.1 Coding c.*462A>T 68

T downstream_gene_variant MODIFIER rzoD b4510 transcript ABD18640.1 Coding c.*183A>T 127

U00096 gene 578600- 578893

- borD b0557 ybcU EcoGene:EG13637

U00096 CDS 578600- 578893

- borD b0557 ybcU EcoGene:EG13637 Phage or Prophage Related bacteriophage lambda Bor protein homolog 1 11 DLP12 prophage; putative lipoprotein AAC73658.1

RESULTS_MG1655

31 ^CHROM ^POS ^{ID REF ALT}

U00096 602184 . G A

A missense_variant MODERATE pheP b0576 transcript AAC73677.1 Coding 1/1 c.226G>A p.Glu76Lys 226/1377 226/1377 76/458 U00096 gene 601959-

603335

+ pheP b0576 JW0565 EcoGene:EG10708

U00096 CDS 601959- 603335

+ pheP b0576 JW0565 EcoGene:EG10708 transport; Transport of small molecules: Amino acids, amines phenylalanine- specific transport system; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009094 - L-phenylalanine biosynthetic process; GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 phenylalanine transporter AAC73677.1

RESULTS_MG1655

32 ^CHROM ^POS ^{ID REF ALT}

U00096 649472 . G A

A stop_gained HIGH citF b0615 transcript AAC73716.1 Coding 1/1 c.100C>T p.Gln34* 100/1533 100/1533 34/510

A downstream_gene_variant MODIFIER citE b0616 transcript AAC73717.2 Coding c.*909C>T 110

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_MG1655

33 ^CHROM ^POS ^{ID REF ALT}

U00096 651373 . G A

A missense_variant MODERATE citC b0618 transcript AAC73719.2 Coding 1/1 c.484C>T p.Arg162Cys 484/1059 484/1059 162/352 U00096 gene 650798-

651856

- citC b0618 ybeO EcoGene:EG13645

U00096 CDS 650798- 651856

- citC b0618 ybeO EcoGene:EG13645 enzyme; Central intermediary metabolism: Pool, multipurpose conversions citrate lyase synthetase (citrate (pro-3S)-lyase ligase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006464 - protein modification process 1 11 citrate lyase ligase; [citrate [pro-3S]-lyase] ligase AAC73719.2 6.2.1.22

RESULTS_MG1655

RESULTS_CIM5H 222.0 . 31 -1.173936e+00 1 2 0,1,13,17 60 -82 1,0.33,1,0.48 2.047399e-01 GT:PL:GQ 1/1:255,55,0:99

34 ^CHROM ^POS ^{ID REF ALT}

U00096 693279 . G A

A missense_variant MODERATE ybeZ b0660 transcript AAC73761.2 Coding 1/1 c.100C>T p.Arg34Cys 100/1041 100/1041 34/346 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_MG1655

(8)

35 ^CHROM ^POS ^{ID REF ALT}

U00096 734251 . C T

T missense_variant MODERATE rhsO b0703 transcript b0703 Coding 1/1 c.119C>T p.Ala40Val 119/1521 119/1521 40/506 WARNING_TRANSCRIPT_NO_START_CODON T downstream_gene_variant MODIFIER ybfB b0702 transcript AAC73796.1 Coding c.*327C>T 149

U00096 gene 734133-735653 + rhsO b0703 ybfO EcoGene:EG13661

U00096 CDS 734133-735653 + rhsO b0703 ybfO EcoGene:EG13661 pseudogene, Rhs family 1 11

RESULTS_MG1655

36 ^CHROM ^POS ^{ID REF ALT}

U00096 747445 . G T

T missense_variant MODERATE abrB b0715 transcript AAC73809.2 Coding 1/1 c.325C>A p.Pro109Thr 325/1047 325/1047 109/348 U00096 gene 746723-

747769

- abrB b0715 ybgN EcoGene:EG13310

U00096 CDS 746723- 747769

- abrB b0715 ybgN EcoGene:EG13310 putative transport; Not classified putative transport protein; GO_component:

GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 regulator of aidB expression; inner membrane protein AAC73809.2

RESULTS_MG1655

37 ^CHROM ^POS ^{ID REF ALT}

U00096 812748 . C T

T missense_variant MODERATE bioD b0778 transcript AAC73865.1 Coding 1/1 c.479C>T p.Ala160Val 479/678 479/678 160/225 U00096 gene 812270-

812947

+ bioD b0778 JW0761 EcoGene:EG10120

U00096 CDS 812270- 812947

+ bioD b0778 JW0761 EcoGene:EG10120 enzyme; Biosynthesis of cofactors, carriers: Biotin GO_process: GO:0009102 - biotin biosynthetic process 1 11 dethiobiotin synthetase AAC73865.1 6.3.3.3

RESULTS_MG1655

38 ^CHROM ^POS ^{ID REF ALT}

U00096 862428 . A T

T missense_variant MODERATE ybiW b0823 transcript AAC73910.1 Coding 1/1 c.179T>A p.Leu60Gln 179/2433 179/2433 60/810

T downstream_gene_variant MODIFIER ybiY b0824 transcript AAC73911.2 Coding c.*900T>A 184

U00096 gene 860174- 862606

- ybiW b0823 pflF EcoGene:EG13328

U00096 CDS 860174- 862606

- ybiW b0823 pflF EcoGene:EG13328 putative enzyme; Not classified GO_process: GO:0006113 - fermentation 1 11 putative pyruvate formate lyase AAC73910.1

RESULTS_MG1655

39 ^CHROM ^POS ^{ID REF ALT}

U00096 871477 . C T

T stop_gained HIGH gsiC b0831 transcript AAC73918.1 Coding 1/1 c.511C>T p.Gln171* 511/921 511/921 171/306 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_MG1655

CHROM POS ID REF ALT

(9)

40 U00096 895153 . G A

A missense_variant MODERATE potG b0855 transcript AAC73942.2 Coding 1/1 c.163G>A p.Gly55Ser 163/1134 163/1134 55/377 U00096 gene 894991-

896124

+ potG b0855 JW5818 EcoGene:EG11630

U00096 CDS 894991- 896124

+ potG b0855 JW5818 EcoGene:EG11630 transport; Transport of small molecules: Amino acids, amines ATP-binding component of putrescine transport system; GO_component: GO:0005737 - cytoplasm; 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 ATPase AAC73942.2

RESULTS_MG1655

41 ^CHROM ^POS ^{ID REF ALT}

U00096 916809 . C A

A missense_variant MODERATE ybjD b0876 transcript AAC73963.1 Coding 1/1 c.337C>A p.Arg113Ser 337/1659 337/1659 113/552 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_MG1655

42 ^CHROM ^POS ^{ID REF ALT}

U00096 937762 . G A

A missense_variant MODERATE lolA b0891 transcript AAC73977.2 Coding 1/1 c.391G>A p.Gly131Ser 391/612 391/612 131/203 U00096 gene 937372-

937983

+ lolA b0891 yzzV EcoGene:EG12684

U00096 CDS 937372- 937983

+ lolA b0891 yzzV EcoGene:EG12684 transport; Protein, peptide secretion periplasmic protein effects translocation of lipoproteins from inner membrane to outer; GO_component: GO:0042597 - periplasmic space 1 11 lipoprotein chaperone AAC73977.2

RESULTS_MG1655

43 ^CHROM ^POS ^{ID REF ALT}

U00096 974632 . C A

A missense_variant MODERATE mukF b0922 transcript AAC74008.1 Coding 1/1 c.314C>A p.Pro105Gln 314/1323 314/1323 105/440 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_MG1655

44 ^CHROM ^POS ^{ID REF ALT}

U00096 1008814 . C T

T missense_variant MODERATE rlmL b0948 transcript AAC74034.1 Coding 1/1 c.971C>T p.Ala324Val 971/2109 971/2109 324/702 U00096 gene 1007844-

1009952

+ rlmL b0948 ycbY EcoGene:EG13717

U00096 CDS 1007844- 1009952

+ rlmL b0948 ycbY EcoGene:EG13717 enzyme; rRNA modification putative oxidoreductase 1 11 23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM-dependent AAC74034.1

RESULTS_MG1655

(10)

45 ^CHROM U00096 1047811 . ^POS ^{ID REF ALT} C T

T missense_variant MODERATE gfcD b0984 transcript AAC74069.1 Coding 1/1 c.135G>A p.Met45Ile 135/2097 135/2097 45/698

T downstream_gene_variant MODIFIER gfcC b0985 transcript AAC74070.1 Coding c.*747G>A 134

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_MG1655

46 ^CHROM ^POS ^{ID REF ALT}

U00096 1069647 . A G

G missense_variant MODERATE rutG b1006 transcript AAC74091.2 Coding 1/1 c.193T>C p.Ser65Pro 193/1329 193/1329 65/442 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_MG1655

47 ^CHROM ^POS ^{ID REF ALT}

U00096 1110221 . A G

G missense_variant MODERATE opgG b1048 transcript AAC74132.1 Coding 1/1 c.887A>G p.His296Arg 887/1536 887/1536 296/511 U00096 gene 1109335-

1110870

+ opgG b1048 mdoG EcoGene:EG11885

U00096 CDS 1109335- 1110870

+ opgG b1048 mdoG EcoGene:EG11885 enzyme; Osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic glucans biosynthesis protein; GO_component: GO:0042597 - periplasmic space; GO_process: GO:0009250 - glucan biosynthetic process; GO_process: GO:0006970 - response to osmotic stress 1 11 OPG biosynthetic periplasmic beta-1,6 branching glycosyltransferase AAC74132.1

RESULTS_MG1655

48 ^CHROM ^POS ^{ID REF ALT}

U00096 1113730 . T A

A missense_variant MODERATE yceK b1050 transcript AAC74134.1 Coding 1/1 c.152T>A p.Ile51Asn 152/228 152/228 51/75

A downstream_gene_variant MODIFIER msyB b1051 transcript AAC74135.2 Coding c.*375A>T 77

U00096 gene 1113579-1113806 + yceK b1050 JW5151 EcoGene:EG12689

U00096 CDS 1113579-1113806 + yceK b1050 JW5151 EcoGene:EG12689 1 11 outer membrane integrity lipoprotein AAC74134.1

RESULTS_MG1655

49 ^CHROM ^POS ^{ID REF ALT}

U00096 1183061 . G A

A missense_variant MODERATE potC b1124 transcript AAC74208.1 Coding 1/1 c.560C>T p.Ala187Val 560/795 560/795 187/264 U00096 gene 1182826-

1183620

- potC b1124 JW1110 EcoGene:EG10751

U00096 CDS 1182826- 1183620

- potC b1124 JW1110 EcoGene:EG10751 transport; Transport of small molecules: Amino acids, amines spermidine/putrescine transport system permease; membrane component of ABC superfamily; GO_component:

GO:0006596 - polyamine biosynthetic process; GO_process: GO:0009310 - amine catabolic process 1 11 spermidine/putrescine ABC transporter permease AAC74208.1

RESULTS_MG1655

(11)

50 ^CHROM ^POS ^{ID REF ALT}

U00096 1183867 . G A

A missense_variant MODERATE potB b1125 transcript AAC74209.1 Coding 1/1 c.578C>T p.Thr193Met 578/828 578/828 193/275 U00096 gene 1183617-

1184444

- potB b1125 JW1111 EcoGene:EG10750

U00096 CDS 1183617- 1184444

- potB b1125 JW1111 EcoGene:EG10750 transport; Transport of small molecules: Amino acids, amines spermidine/putrescine transport system permease; membrane component of ABC superfamily; GO_component:

RESULTS_MG1655

51 ^CHROM ^POS ^{ID REF ALT}

U00096 1184272 . G T

T stop_gained HIGH potB b1125 transcript AAC74209.1 Coding 1/1 c.173C>A p.Ser58* 173/828 173/828 58/275

T downstream_gene_variant MODIFIER potA b1126 transcript AAC74210.1 Coding c.*1137C>A 186

U00096 gene 1183617- 1184444

- potB b1125 JW1111 EcoGene:EG10750

U00096 CDS 1183617- 1184444

- potB b1125 JW1111 EcoGene:EG10750 transport; Transport of small molecules: Amino acids, amines spermidine/putrescine transport system permease; membrane component of ABC superfamily; GO_component:

RESULTS_MG1655

52 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1199498 . CAAAAA CAAAA

frameshift_variant HIGH lit b1139 transcript AAC74223.1 Coding 1/1 c.809delA p.Asn270fs 809/894 809/894 270/297

downstream_gene_variant MODIFIER intE b1140 transcript AAC74224.1 Coding c.*1128delT 176

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_MG1655

RESULTS_CIM5H 94.5 . 17 1 2 0,0,11,3 58 -76.5 1.665297e-01 11,0.647059 GT:PL:GQ 1/1:135,42,0:81

53 ^CHROM ^POS ^{ID REF ALT}

U00096 1199503 . A T

T missense_variant MODERATE lit b1139 transcript AAC74223.1 Coding 1/1 c.809A>T p.Asn270Ile 809/894 809/894 270/297

T downstream_gene_variant MODIFIER intE b1140 transcript AAC74224.1 Coding c.*1128T>A 176

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_MG1655

RESULTS_CIM5H 27.0 . 16 2.556157e+00 0.5 1 10,3,2,1 59 30 1,1,1,0.0013 2.570870e-02 GT:PL:GQ 0/1:57,0,227:60

54 ^CHROM ^POS ^{ID REF ALT}

U00096 1238385 . T G

G missense_variant MODERATE dadA b1189 transcript AAC74273.1 Coding 1/1 c.815T>G p.Leu272Arg 815/1299 815/1299 272/432 U00096 gene 1237571- + dadA b1189 JW1178 EcoGene:EG11407

(12)

1238869 U00096 CDS 1237571-

1238869

+ dadA b1189 JW1178 EcoGene:EG11407 enzyme; Degradation of small molecules: Amino acids D-amino acid dehydrogenase subunit; GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 D-amino acid dehydrogenase AAC74273.1 1.4.99.1

RESULTS_MG1655

55 ^CHROM ^POS ^{ID REF ALT}

U00096 1239692 . T C

C missense_variant MODERATE dadX b1190 transcript AAC74274.1 Coding 1/1 c.814T>C p.Tyr272His 814/1071 814/1071 272/356 U00096 gene 1238879-

1239949

+ dadX b1190 msuA? EcoGene:EG11408

U00096 CDS 1238879- 1239949

+ dadX b1190 msuA? EcoGene:EG11408 enzyme; Degradation of small molecules: Amino acids alanine racemase 2, catabolic; GO_process: GO:0009063 - cellular amino acid catabolic process; GO_process: GO:0006523 - alanine biosynthetic process 1 11 alanine racemase, catabolic, PLP-binding AAC74274.1 5.1.1.1

RESULTS_MG1655

56 ^CHROM ^POS ^{ID REF ALT}

U00096 1257004 . A T

T missense_variant MODERATE ychF b1203 transcript AAC74287.1 Coding 1/1 c.809T>A p.Ile270Asn 809/1092 809/1092 270/363 U00096 gene 1256721-

1257812

- ychF b1203 JW1194 EcoGene:EG11404

U00096 CDS 1256721- 1257812

- ychF b1203 JW1194 EcoGene:EG11404 enzyme; Not classified putative GTP-binding protein 1 11 catalase inhibitor protein; ATPase, K+-dependent, ribosome-associated AAC74287.1

RESULTS_MG1655

57 ^CHROM ^POS ^{ID REF ALT}

U00096 1290291 . A C

C missense_variant MODERATE rssB b1235 transcript AAC74317.1 Coding 1/1 c.50A>C p.Gln17Pro 50/1014 50/1014 17/337

C downstream_gene_variant MODIFIER rssA b1234 transcript AAC74316.2 Coding c.*906A>C 141

U00096 gene 1290242- 1291255

+ rssB b1235 ychL EcoGene:EG12121

U00096 CDS 1290242- 1291255

+ rssB b1235 ychL EcoGene:EG12121 regulator; Basic proteins - synthesis, modification Hnr protein; GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0006350 - transcription 1 11 PcnB-degradosome interaction factor; response regulator AAC74317.1

RESULTS_MG1655

58 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1304332 . ATTTT ATTTTT

T frameshift_variant HIGH oppC b1245 transcript AAC74327.1 Coding 1/1 c.503dupT p.Val169fs 504/909 504/909 168/302 U00096 gene 1303834-

1304742

+ oppC b1245 stkB EcoGene:EG10676

U00096 CDS 1303834- 1304742

+ oppC b1245 stkB EcoGene:EG10676 transport; Not classified homolog of Salmonella oligopeptide transport permease protein; membrane component of ABC superfamily; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0000270 - peptidoglycan metabolic process 1 11 oligopeptide ABC transporter permease AAC74327.1

RESULTS_MG1655

59 ^CHROM ^POS ^{ID REF ALT}

U00096 1311270 . T C

(13)

C missense_variant MODERATE tonB b1252 transcript AAC74334.1 Coding 1/1 c.182T>C p.Val61Ala 182/720 182/720 61/239 U00096 gene 1311089-

1311808

+ tonB b1252 T1rec EcoGene:EG11012

U00096 CDS 1311089- 1311808

+ tonB b1252 T1rec EcoGene:EG11012 membrane; Transport of small molecules: Cations energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins; GO_component: GO:0009274 - peptidoglycan-based cell wall;

GO_component: GO:0019866 - organelle inner membrane 1 11 membrane spanning protein in TonB-ExbB-ExbD transport complex AAC74334.1

RESULTS_MG1655

60 ^CHROM ^POS ^{ID REF ALT}

U00096 1319991 . G A

A missense_variant MODERATE trpD b1263 transcript AAC74345.1 Coding 1/1 c.1394C>T p.Pro465Leu 1394/1596 1394/1596 465/531 U00096 gene 1319789-

1321384

- trpD b1263 trpGD EcoGene:EG11027

U00096 CDS 1319789- 1321384

- trpD b1263 trpGD EcoGene:EG11027 enzyme; Amino acid biosynthesis: Tryptophan anthranilate synthase component II, glutamine amidotransferase and phosphoribosylanthranilate transferase; GO_component: GO:0005737 - cytoplasm;

GO_process: GO:0000162 - tryptophan biosynthetic process 1 11 fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase AAC74345.1 4.1.3.27

RESULTS_MG1655

61 ^CHROM ^POS ^{ID REF ALT}

U00096 1373097 . G A

A missense_variant MODERATE ycjN b1310 transcript AAC74392.1 Coding 1/1 c.1189G>A p.Val397Met 1189/1293 1189/1293 397/430

A upstream_gene_variant MODIFIER ycjO b1311 transcript AAC74393.1 Coding c.-1G>A 125

U00096 gene 1371909- 1373201

+ ycjN b1310 JW1303 EcoGene:EG13911

U00096 CDS 1371909- 1373201

+ ycjN b1310 JW1303 EcoGene:EG13911 putative transport; Not classified GO_component: GO:0042597 - periplasmic space 1 11 putative ABC sugar transporter periplasmic binding protein AAC74392.1

RESULTS_MG1655

62 ^CHROM ^POS ^{ID REF ALT}

U00096 1411109 . A T

T missense_variant MODERATE ttcA b1344 transcript AAC74426.1 Coding 1/1 c.840T>A p.Asp280Glu 840/936 840/936 280/311 U00096 gene 1411013-

1411948

- ttcA b1344 ydaO EcoGene:EG13357

U00096 CDS 1411013- 1411948

- ttcA b1344 ydaO EcoGene:EG13357 putative enzyme; Not classified 1 11 tRNA s(2)C32 thioltransferase, iron sulfur cluster protein AAC74426.1

RESULTS_MG1655

63 ^CHROM ^POS ^{ID REF ALT}

U00096 1452220 . G A

A missense_variant MODERATE paaZ b1387 transcript AAC74469.1 Coding 1/1 c.1423C>T p.Pro475Ser 1423/2046 1423/2046 475/681 U00096 gene 1451597-

1453642

- paaZ b1387 ydbN EcoGene:EG13735

U00096 CDS 1451597- 1453642

- paaZ b1387 ydbN EcoGene:EG13735 enzyme; Phenylacetic acid degradation GO_process: GO:0016052 - carbohydrate catabolic process 1 11 oxepin-CoA hydrolase and 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase AAC74469.1

RESULTS_MG1655

CHROM POS ID REF ALT

(14)

64 U00096 1475586 . C T

T missense_variant MODERATE ydbD b1407 transcript AAC74489.2 Coding 1/1 c.443C>T p.Pro148Leu 443/2307 443/2307 148/768 U00096 gene 1475144-

1477450

+ ydbD b1407 JW5221 EcoGene:EG11310

U00096 CDS 1475144- 1477450

+ ydbD b1407 JW5221 EcoGene:EG11310 1 11 PF10971 family putative periplasmic methylglyoxal resistance protein AAC74489.2

RESULTS_MG1655

65 ^CHROM ^POS ^{ID REF ALT}

U00096 1506257 . C T

T missense_variant MODERATE ydcN b1434 transcript AAC74516.1 Coding 1/1 c.86C>T p.Ala29Val 86/537 86/537 29/178

T upstream_gene_variant MODIFIER ydcO b1433 transcript AAC74515.2 Coding c.-1G>A 177

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_MG1655

66 ^CHROM ^POS ^{ID REF ALT}

U00096 1513132 . G A

A missense_variant MODERATE ydcT b1441 transcript AAC74523.1 Coding 1/1 c.316G>A p.Val106Met 316/1014 316/1014 106/337 U00096 gene 1512817-

1513830

+ ydcT b1441 JW1436 EcoGene:EG13763

U00096 CDS 1512817- 1513830

+ ydcT b1441 JW1436 EcoGene:EG13763 putative transport; Not classified ATP-binding component of ABC superfamily;

GO_component: GO:0005737 - cytoplasm 1 11 putative ABC transporter ATPase AAC74523.1

RESULTS_MG1655

67 ^CHROM ^POS ^{ID REF ALT}

U00096 1539530 . A G

G missense_variant MODERATE narZ b1468 transcript AAC74550.1 Coding 1/1 c.3061T>C p.Ser1021Pro 3061/3741 3061/3741 1021/1246 U00096 gene 1538850-

1542590

- narZ b1468 JW1463 EcoGene:EG10648

U00096 CDS 1538850- 1542590

- narZ b1468 JW1463 EcoGene:EG10648 enzyme; Energy metabolism, carbon: Anaerobic respiration GO_component:

GO:0009061 - anaerobic respiration 1 11 nitrate reductase 2 (NRZ), alpha subunit AAC74550.1 1.7.99.4

RESULTS_MG1655

68 ^CHROM ^POS ^{ID REF ALT}

U00096 1582328 . T C

C missense_variant MODERATE ydeN b1498 transcript AAC74571.2 Coding 1/1 c.197A>G p.Asp66Gly 197/1683 197/1683 66/560 U00096 gene 1580842-

1582524

- ydeN b1498 JW5243 EcoGene:EG13796

U00096 CDS 1580842- 1582524

- ydeN b1498 JW5243 EcoGene:EG13796 putative enzyme; Not classified putative sulfatase; GO_process: GO:0006790 - sulfur metabolic process 1 11 putative Ser-type periplasmic non-aryl sulfatase AAC74571.2

RESULTS_MG1655

CHROM POS ID REF ALT

(15)

69 U00096 1615877 . A T

T missense_variant MODERATE yneK b1527 transcript AAC74600.1 Coding 1/1 c.115A>T p.Thr39Ser 115/1116 115/1116 39/371

T downstream_gene_variant MODIFIER yneJ b1526 transcript AAC74599.1 Coding c.*882A>T 192

U00096 gene 1615763-1616878 + yneK b1527 JW1520 EcoGene:EG13819

U00096 CDS 1615763-1616878 + yneK b1527 JW1520 EcoGene:EG13819 1 11 uncharacterized protein AAC74600.1

RESULTS_MG1655

70 ^CHROM ^POS ^{ID REF ALT}

U00096 1621770 . A G

G missense_variant MODERATE ydeE b1534 transcript AAC74607.1 Coding 1/1 c.439A>G p.Ile147Val 439/1188 439/1188 147/395 U00096 gene 1621332-

1622519

+ ydeE b1534 ydeF EcoGene:EG11640

U00096 CDS 1621332- 1622519

+ ydeE b1534 ydeF EcoGene:EG11640 putative transport; Not classified putative transport protein; GO_component:

GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 putative transporter AAC74607.1

RESULTS_MG1655

71 ^CHROM ^POS ^{ID REF ALT}

U00096 1625496 . A G

G missense_variant MODERATE dcp b1538 transcript AAC74611.1 Coding 1/1 c.1885T>C p.Phe629Leu 1885/2046 1885/2046 629/681 U00096 gene 1625335-

1627380

- dcp b1538 JW1531 EcoGene:EG10212

U00096 CDS 1625335- 1627380

- dcp b1538 JW1531 EcoGene:EG10212 enzyme; Degradation of proteins, peptides, glyco 1 11 dipeptidyl carboxypeptidase II AAC74611.1 3.4.15.5

RESULTS_MG1655

72 ^CHROM ^POS ^{ID REF ALT}

U00096 1634147 . G A

A missense_variant MODERATE pinQ b1545 transcript AAC74618.1 Coding 1/1 c.526G>A p.Glu176Lys 526/591 526/591 176/196

A downstream_gene_variant MODIFIER tfaQ b1546 transcript AAC74619.1 Coding c.*576C>T 163

A intron_variant MODIFIER ydfJ b4600 transcript b4600 Coding 1/1 c.85-1862C>T U00096 gene 1633622-

1634212

+ pinQ b1545 ydfL EcoGene:EG13824

U00096 CDS 1633622- 1634212

+ pinQ b1545 ydfL EcoGene:EG13824 Phage or Prophage Related 1 11 Qin prophage; putative site-specific recombinase AAC74618.1

RESULTS_MG1655

RESULTS_CIM5H 83.3 . 18 6.900097e-01 1 2 4,1,8,5 17 -42 0.61,1,1,0.001 1.558832e-01 GT:PL:GQ 1/1:116,15,0:27

73 ^CHROM ^POS ^{ID REF ALT}

U00096 1662456 . T A

A stop_gained HIGH ynfF b1588 transcript AAC74660.4 Coding 1/1 c.1901T>A p.Leu634* 1901/2424 1901/2424 634/807 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_MG1655

(16)

74 ^CHROM U00096 1684071 . ^POS ^{ID REF ALT} T C

C missense_variant MODERATE rstB b1609 transcript AAC74681.1 Coding 1/1 c.1190T>C p.Ile397Thr 1190/1302 1190/1302 397/433

C upstream_gene_variant MODIFIER tus b1610 transcript AAC74682.1 Coding c.-1T>C 188

U00096 gene 1682882- 1684183

+ rstB b1609 uspT EcoGene:EG11233

U00096 CDS 1682882- 1684183

+ rstB b1609 uspT EcoGene:EG11233 regulator; Global regulatory functions sensor histidine protein kinase (RstA regulator); 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 of RstAB two- component system AAC74681.1

RESULTS_MG1655

RESULTS_CIM5H 12.3 . 33 -3.133916e-01 0.5 1 13,15,3,1 60 15.1 0.6,1,1,1 5.619835e-02 GT:PL:GQ 0/1:42,0,255:44

75 ^CHROM ^POS ^{ID REF ALT}

U00096 1706877 . A T

T missense_variant MODERATE rsxB b1628 transcript AAC74700.1 Coding 1/1 c.530A>T p.Asp177Val 530/579 530/579 177/192

T upstream_gene_variant MODIFIER rsxC b1629 transcript AAC74701.1 Coding c.-1A>T 42

U00096 gene 1706348- 1706926

+ rsxB b1628 ydgM EcoGene:EG13934

U00096 CDS 1706348- 1706926

+ rsxB b1628 ydgM EcoGene:EG13934 GO_function: GO:0009055 - electron carrier activity 1 11 SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein AAC74700.1

RESULTS_MG1655

76 ^CHROM ^POS ^{ID REF ALT}

U00096 1722167 . C T

T missense_variant MODERATE ydhK b1645 transcript AAC74717.1 Coding 1/1 c.47C>T p.Ala16Val 47/2013 47/2013 16/670

T downstream_gene_variant MODIFIER ydhJ b1644 transcript AAC74716.2 Coding c.*858C>T 46

U00096 gene 1722121- 1724133

+ ydhK b1645 JW1637 EcoGene:EG13945

U00096 CDS 1722121- 1724133

+ ydhK b1645 JW1637 EcoGene:EG13945 1 11 putative efflux protein (PET) component of YdhJK efflux pump AAC74717.1

RESULTS_MG1655

77 ^CHROM ^POS ^{ID REF ALT}

U00096 1730699 . C T

T missense_variant MODERATE lhr b1653 transcript AAC74725.1 Coding 1/1 c.1613C>T p.Ala538Val 1613/4617 1613/4617 538/1538 U00096 gene 1729087-

1733703

+ lhr b1653 rhlF EcoGene:EG11548

U00096 CDS 1729087- 1733703

+ lhr b1653 rhlF EcoGene:EG11548 enzyme; DNA - replication, repair, restriction/modification member of ATP-dependent helicase superfamily II; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006261 - DNA-dependent DNA replication 1 11 putative ATP-dependent helicase AAC74725.1

RESULTS_MG1655

78 ^CHROM ^POS ^{ID REF ALT}

U00096 1738556 . A G

G missense_variant MODERATE purR b1658 transcript AAC74730.1 Coding 1/1 c.713A>G p.His238Arg 713/1026 713/1026 238/341 U00096 gene 1737844-

1738869

+ purR b1658 JW1650 EcoGene:EG10800

U00096 CDS 1737844- 1738869

+ purR b1658 JW1650 EcoGene:EG10800 regulator; Purine ribonucleotide biosynthesis transcriptional repressor for pur regulon, glyA, glnB, prsA, speA; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0016564 - transcription repressor activity; GO_process: GO:0006164 - purine nucleotide biosynthetic process; GO_process: GO:0006596 - polyamine biosynthetic process; GO_process: GO:0000105 - histidine biosynthetic process; GO_process: GO:0009063 - cellular amino acid catabolic process; GO_process: GO:0006545 - glycine biosynthetic process; GO_process:

GO:0006807 - nitrogen compound metabolic process; GO_process: GO:0006221 - pyrimidine nucleotide biosynthetic

Non synonimous mutations found in sample: CIM5H