Non synonimous mutations found in sample: CIQ1G

(1)

Non synonimous mutations found in sample: CIQ1G

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 13901 . A G

G missense_variant MODERATE dnaK b0014 transcript AAC73125.1 Coding 1/1 c.1739A>G p.Asp580Gly 1739/1917 1739/1917 580/638 U00096 gene 12163-

14079

+ dnaK b0014 seg EcoGene:EG10241

U00096 CDS 12163- 14079

+ dnaK b0014 seg EcoGene:EG10241 factor; Chaperones chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006457 - protein folding; GO_process:

GO:0006970 - response to osmotic stress 1 11 chaperone Hsp70, with co-chaperone DnaJ AAC73125.1

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

RESULTS_dnaQ

RESULTS_CIQ1G 222.0 . 34 1 2 0,0,16,18 60 -129 2.959904e-01 GT:PL:GQ 1/1:255,102,0:99

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

3 CHROM POS ID REF ALT U00096 63698 . A G

G missense_variant MODERATE polB b0060 transcript AAC73171.1 Coding 1/1 c.2083T>C p.Tyr695His 2083/2352 2083/2352 695/783 U00096 gene 63429-

65780

- polB b0060 JW0059 EcoGene:EG10747

U00096 CDS 63429- 65780

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

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

RESULTS_dnaQ

4 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

5 CHROM POS ID REF ALT U00096 78630 . CGGGGG CGGGG

frameshift_variant HIGH setA b0070 transcript AAT48123.1 Coding 1/1 c.1015delG p.Ala339fs 1015/1179 1015/1179 339/392 U00096 gene 77621-

78799

+ setA b0070 yabM EcoGene:EG11754

(2)

U00096 CDS 77621- 78799

+ setA b0070 yabM EcoGene:EG11754 putative transport; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_function: GO:0015543 - lactose/glucose efflux transporter activity; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 broad specificity sugar efflux system AAT48123.1

RESULTS_dnaQ

RESULTS_CIQ1G 136.0 . 18 1 2 0,0,6,12 60 -88.5 1.657323e-01 18,1.000000 GT:PL:GQ 1/1:177,54,0:99

6 CHROM POS ID REF ALT U00096 86260 . G A

A missense_variant MODERATE ilvI b0077 transcript AAC73188.2 Coding 1/1 c.631G>A p.Val211Ile 631/1725 631/1725 211/574 U00096 gene 85630-

87354

+ ilvI b0077 JW0076 EcoGene:EG10500

U00096 CDS 85630- 87354

+ ilvI b0077 JW0076 EcoGene:EG10500 enzyme; Amino acid biosynthesis: Isoleucine, Valine acetolactate synthase III, valine sensitive, large subunit 1 11 acetolactate synthase 3 large subunit AAC73188.2 2.2.1.6 N-terminus verified by Edman degradation: PMID 3881131,9298646

RESULTS_dnaQ

RESULTS_CIQ1G 94.0 . 42 1.134967e+00 0.5 1 14,19,5,3 60 97 0.44,1,1,0.27 1.221123e-01 GT:PL:GQ 0/1:124,0,255:99

7 CHROM POS ID REF ALT U00096 89913 . A G

G missense_variant MODERATE mraZ b0081 transcript AAC73192.1 Coding 1/1 c.280A>G p.Ile94Val 280/459 280/459 94/152

G upstream_gene_variant MODIFIER rsmH b0082 transcript AAC73193.1 Coding c.-1A>G 181

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

RESULTS_dnaQ

8 ^CHROM ^POS ^ID ^REF ^ALT

U00096 102906 . GCCCC GCCC

frameshift_variant HIGH ddlB b0092 transcript AAC73203.1 Coding 1/1 c.678delC p.Pro226fs 678/921 678/921 226/306 U00096 gene 102233-

103153

+ ddlB b0092 JW0090 EcoGene:EG10214

U00096 CDS 102233- 103153

+ ddlB b0092 JW0090 EcoGene:EG10214 enzyme; Murein sacculus, peptidoglycan D-alanine-D-alanine ligase B, affects cell division; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm;

GO_process: GO:0009252 - peptidoglycan biosynthetic process 1 11 D-alanine:D-alanine ligase AAC73203.1 6.3.2.4

RESULTS_dnaQ

RESULTS_CIQ1G 8.18 . 23 0.5 1 11,7,3,2 60 10.8 1,0.0028,1,1 1.876543e-01 4,0.173913 GT:PL:GQ 0/1:45,0,177:47

9 ^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;

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

RESULTS_dnaQ

10 ^CHROM ^POS ^{ID REF ALT}

U00096 150833 . A G

G missense_variant MODERATE yadC b0135 transcript AAC73246.1 Coding 1/1 c.121T>C p.Ser41Pro 121/1239 121/1239 41/412

G downstream_gene_variant MODIFIER yadK b0136 transcript AAC73247.1 Coding c.*597T>C 170

U00096 gene 149715- - yadC b0135 JW0131 EcoGene:EG11678

(3)

150953 U00096 CDS 149715-

150953

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

RESULTS_dnaQ

11 ^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

RESULTS_CIQ1G 150.0 . 25 1 2 0,0,13,11 60 -107 2.447307e-01 23,0.920000 GT:PL:GQ 1/1:191,72,0:99

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

13 ^CHROM ^POS ^{ID REF ALT}

U00096 183729 . C T

T missense_variant MODERATE yaeH b0163 transcript AAC73274.1 Coding 1/1 c.367G>A p.Glu123Lys 367/387 367/387 123/128

T downstream_gene_variant MODIFIER cdaR b0162 transcript AAC73273.2 Coding c.*1158C>T 109

U00096 gene 183709- 184095

- yaeH b0163 JW0159 EcoGene:EG12336

U00096 CDS 183709- 184095

- yaeH b0163 JW0159 EcoGene:EG12336 putative structure; Not classified putative structural protein 1 11 UPF0325 family protein AAC73274.1

RESULTS_dnaQ

14 ^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

15 ^CHROM ^POS ^{ID REF ALT}

U00096 208804 . C A

A missense_variant MODERATE accA b0185 transcript AAC73296.1 Coding 1/1 c.184C>A p.Gln62Lys 184/960 184/960 62/319

(4)

A downstream_gene_variant MODIFIER dnaE b0184 transcript AAC73295.1 Coding c.*3483C>A 196 U00096 gene 208621-

209580

+ accA b0185 JW0180 EcoGene:EG11647

U00096 CDS 208621- 209580

+ accA b0185 JW0180 EcoGene:EG11647 enzyme; Fatty acid and phosphatidic acid biosynthesis acetylCoA carboxylase, carboxytransferase component, alpha subunit; GO_component: GO:0005737 - cytoplasm 1 11 acetyl-CoA carboxylase, carboxytransferase, alpha subunit AAC73296.1 6.4.1.2

RESULTS_dnaQ

RESULTS_CIQ1G 16.1 . 42 -1.165177e-01 0.5 1 20,17,3,2 60 19.1 1,1,1,0.17 8.054322e-02 GT:PL:GQ 0/1:46,0,255:49

16 ^CHROM ^POS ^ID ^REF ^ALT

U00096 215726 . ATTTTT ATTTT

frameshift_variant HIGH nlpE b0192 transcript AAC73303.1 Coding 1/1 c.463delT p.Tyr155fs 463/711 463/711 155/236 U00096 gene 215269-

215979

+ nlpE b0192 JW0188 EcoGene:EG12137

U00096 CDS 215269- 215979

+ nlpE b0192 JW0188 EcoGene:EG12137 putative transport; Detoxification copper homeostasis protein (lipoprotein);

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane;

GO_process: GO:0006805 - xenobiotic metabolic process 1 11 lipoprotein involved with copper homeostasis and adhesion AAC73303.1

RESULTS_dnaQ

17 ^CHROM ^POS ^{ID REF ALT}

U00096 221842 . C T

T missense_variant MODERATE metN b0199 transcript AAC73310.1 Coding 1/1 c.804G>A p.Met268Ile 804/1032 804/1032 268/343 U00096 gene 221614-

222645

- metN b0199 metD EcoGene:EG11621

U00096 CDS 221614- 222645

- metN b0199 metD EcoGene:EG11621 transport; Transport of small molecules: Amino acids, amines D- and L-methionine transport protein (ABC superfamily, atp_bind); GO_component: GO:0005737 - cytoplasm 1 11 DL-methionine transporter subunit AAC73310.1

RESULTS_dnaQ

18 ^CHROM ^POS ^ID ^REF ^ALT

U00096 231186 . CGGGG CGGG

frameshift_variant HIGH yafD b0209 transcript AAC73314.1 Coding 1/1 c.69delG p.Gly23fs 69/801 69/801 23/266 U00096 gene 231122-231922 + yafD b0209 JW5017 EcoGene:EG11650

U00096 CDS 231122-231922 + yafD b0209 JW5017 EcoGene:EG11650 1 11 endo/exonuclease/phosphatase family protein AAC73314.1

RESULTS_dnaQ

19 ^CHROM ^POS ^ID ^REF ^ALT

U00096 238646 . TAAAAAA TAAAAA

frameshift_variant HIGH ykfM b4586 transcript ABP93434.1 Coding 1/1 c.85delT p.Phe29fs 85/480 85/480 29/159

downstream_gene_variant MODIFIER yafU b0218 transcript b0218 Coding c.*357delT 94 WARNING_TRANSCRIPT_NO_START_CODON U00096 gene 238257-

238736

- ykfM b4586 ECK4397 EcoGene:EG14451

U00096 CDS 238257- 238736

- ykfM b4586 ECK4397 EcoGene:EG14451 1 11 lethality reduction protein, putative inner membrane protein ABP93434.1

RESULTS_dnaQ

20 ^CHROM ^POS ^ID ^REF ^ALT

U00096 264712 . TAAAAA TAAAAAA

(5)

A frameshift_variant HIGH ykfG b0247 transcript AAC73350.1 Coding 1/1 c.15_16insT p.Phe6fs 15/477 15/477 5/158

A downstream_gene_variant MODIFIER yafX b0248 transcript AAC73351.1 Coding c.*459_*459insT 30

U00096 gene 264256- 264732

- ykfG b0247 JW0236 EcoGene:EG14331

U00096 CDS 264256- 264732

- ykfG b0247 JW0236 EcoGene:EG14331 Phage or Prophage Related putative DNA repair protein 1 11 CP4-6 prophage;

RadC-like JAB domain protein AAC73350.1

RESULTS_dnaQ

RESULTS_CIQ1G 162.0 . 58 1 2 1,0,20,25 60 -153 0.46,1,1,0.46 3.064910e-01 37,0.637931 GT:PL:GQ 1/1:203,118,0:99

21 ^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

22 ^CHROM ^POS ^{ID REF ALT}

U00096 293374 . A G

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

23 ^CHROM ^POS ^{ID REF ALT}

U00096 293798 . C G

G missense_variant MODERATE yagL b0278 transcript AAC73381.1 Coding 1/1 c.121G>C p.Val41Leu 121/699 121/699 41/232

G downstream_gene_variant MODIFIER yagM b0279 transcript AAC73382.1 Coding c.*855G>C 147

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

RESULTS_CIQ1G 75.0 . 12 -7.642870e-01 0.5 1 3,5,2,2 60 78 1,1,1,1 7.931840e-02 GT:PL:GQ 0/1:105,0,192:99

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

U00096 308079 . ACCC ACC

frameshift_variant HIGH ecpC b0291 transcript AAC73394.1 Coding 1/1 c.1251delG p.Val417fs 1251/2526 1251/2526 417/841 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

25 ^CHROM ^POS ^{ID REF ALT}

U00096 315000 . A G

G missense_variant MODERATE eaeH b0297 transcript b0297 Coding 1/1 c.644A>G p.Tyr215Cys 644/872 644/872 215/289 WARNING_TRANSCRIPT_INCOMPLETE

(6)

U00096 gene 314357- 315228

+ eaeH b0297 JW0291 EcoGene:EG12161

U00096 CDS 314357- 315228

+ eaeH b0297 JW0291 EcoGene:EG12161 pseudogene, attaching and effacing protein homology;factor; Not classified;

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11

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 346595 . GAAAAAA GAAAAA

frameshift_variant HIGH yahO b0329 transcript AAC73432.1 Coding 1/1 c.118delA p.Ile40fs 118/276 118/276 40/91

U00096 gene 346484-346759 + yahO b0329 JW0321 EcoGene:EG13599

U00096 CDS 346484-346759 + yahO b0329 JW0321 EcoGene:EG13599 1 11 periplasmic protein, function unknown, YhcN family AAC73432.1

RESULTS_dnaQ

28 ^CHROM ^POS ^{ID REF ALT}

U00096 387209 . T C

C missense_variant MODERATE tauC b0367 transcript AAC73470.1 Coding 1/1 c.239T>C p.Leu80Pro 239/828 239/828 80/275 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

29 ^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

30 ^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

(7)

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

31 ^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

32 ^CHROM ^POS ^{ID REF ALT}

U00096 398065 . A G

G missense_variant MODERATE yaiW b0378 transcript AAC73481.1 Coding 1/1 c.194A>G p.Glu65Gly 194/1095 194/1095 65/364 U00096 gene 397872-

398966

+ yaiW b0378 JW0369 EcoGene:EG13608

U00096 CDS 397872- 398966

+ yaiW b0378 JW0369 EcoGene:EG13608 1 11 microcin Bac7 uptake protein; outer membrane surface-exposed lipoprotein AAC73481.1

RESULTS_dnaQ

33 ^CHROM ^POS ^{ID REF ALT}

U00096 422936 . A G

G missense_variant MODERATE malZ b0403 transcript AAC73506.2 Coding 1/1 c.419A>G p.Glu140Gly 419/1815 419/1815 140/604 U00096 gene 422518-

424332

+ malZ b0403 JW0393 EcoGene:EG10565

U00096 CDS 422518- 424332

+ malZ b0403 JW0393 EcoGene:EG10565 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process; GO_process: GO:0000272 - polysaccharide catabolic process 1 11 maltodextrin glucosidase AAC73506.2 3.2.1.20

RESULTS_dnaQ

34 ^CHROM ^POS ^{ID REF ALT}

U00096 423601 . A G

G missense_variant MODERATE malZ b0403 transcript AAC73506.2 Coding 1/1 c.1084A>G p.Lys362Glu 1084/1815 1084/1815 362/604 U00096 gene 422518-

424332

+ malZ b0403 JW0393 EcoGene:EG10565

U00096 CDS 422518- 424332

+ malZ b0403 JW0393 EcoGene:EG10565 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0005737 - cytoplasm; GO_process: GO:0016052 - carbohydrate catabolic process; GO_process: GO:0000272 - polysaccharide catabolic process 1 11 maltodextrin glucosidase AAC73506.2 3.2.1.20

RESULTS_dnaQ

35 ^CHROM ^POS ^{ID REF ALT}

U00096 442580 . TGG TG

frameshift_variant HIGH thiI b0423 transcript AAC73526.1 Coding 1/1 c.1034delG p.Gly345fs 1034/1449 1034/1449 345/482

(8)

U00096 gene 441549- 442997

+ thiI b0423 yajK EcoGene:EG13273

U00096 CDS 441549- 442997

+ thiI b0423 yajK EcoGene:EG13273 enzyme; tRNA modification GO_process: GO:0009228 - thiamin biosynthetic process;

GO_process: GO:0009451 - RNA modification 1 11 tRNA s(4)U8 sulfurtransferase AAC73526.1

RESULTS_dnaQ

RESULTS_CIQ1G 214.0 . 38 1 2 0,1,17,18 59 -103 1,1.9e-05,0.43,1 2.215269e-01 35,0.921053 GT:PL:GQ 1/1:255,68,0:99

36 ^CHROM ^POS ^{ID REF ALT}

U00096 450631 . T C

C missense_variant MODERATE cyoB b0431 transcript AAC73534.1 Coding 1/1 c.11A>G p.Lys4Arg 11/1992 11/1992 4/663

C downstream_gene_variant MODIFIER cyoA b0432 transcript AAC73535.1 Coding c.*948A>G 32

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: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 451586 . T C

C missense_variant MODERATE cyoA b0432 transcript AAC73535.1 Coding 1/1 c.25A>G p.Ser9Gly 25/948 25/948 9/315 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:0009060 - aerobic respiration 1 11 cytochrome o ubiquinol oxidase subunit II AAC73535.1 1.10.3.-

RESULTS_dnaQ

RESULTS_CIQ1G 30.0 . 4 -1.111223e+00 0.5 1 1,1,1,1 60 31.6 1,0.21,1,0.053 7.680000e-02 GT:PL:GQ 0/1:60,0,64:62

39 ^CHROM ^POS ^{ID REF ALT}

U00096 453644 . G T

T missense_variant MODERATE yajG b0434 transcript AAC73537.2 Coding 1/1 c.524C>A p.Ala175Asp 524/579 524/579 175/192

T upstream_gene_variant MODIFIER ampG b0433 transcript AAC73536.1 Coding c.-1C>A 99

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_dnaQ

40 ^CHROM ^POS ^{ID REF ALT}

U00096 498947 . A G

(9)

G missense_variant MODERATE hemH b0475 transcript AAC73577.1 Coding 1/1 c.893A>G p.Tyr298Cys 893/963 893/963 298/320

G downstream_gene_variant MODIFIER aes b0476 transcript AAC73578.1 Coding c.*960T>C 67

U00096 gene 498055- 499017

+ hemH b0475 visA EcoGene:EG10431

U00096 CDS 498055- 499017

+ hemH b0475 visA EcoGene:EG10431 enzyme; Biosynthesis of cofactors, carriers: Heme, porphyrin ferrochelatase: final enzyme of heme biosynthesis 1 11 ferrochelatase AAC73577.1 4.99.1.1 N-terminus verified by Edman degradation: PMID 8056770

RESULTS_dnaQ

41 ^CHROM ^POS ^ID ^REF ^ALT

U00096 515320 . TCCCCC TCCCC

frameshift_variant HIGH qmcA b0489 transcript AAC73591.1 Coding 1/1 c.449delG p.Trp150fs 449/918 449/918 150/305 U00096 gene 514856-

515773

- qmcA b0489 ybbK EcoGene:EG13258

U00096 CDS 514856- 515773

- qmcA b0489 ybbK EcoGene:EG13258 putative enzyme; Not classified putative protease; GO_component: GO:0009274 - peptidoglycan-based cell wall 1 11 PHB domain membrane-anchored putative protease AAC73591.1

RESULTS_dnaQ

42 ^CHROM ^POS ^{ID REF ALT}

U00096 517882 . G A

A missense_variant MODERATE ybbN b0492 transcript AAC73594.2 Coding 1/1 c.398C>T p.Ala133Val 398/855 398/855 133/284 U00096 gene 517425-

518279

- ybbN b0492 JW5067 EcoGene:EG13261

U00096 CDS 517425- 518279

- ybbN b0492 JW5067 EcoGene:EG13261 putative enzyme; Not classified putative thioredoxin-like protein 1 11 DnaK co- chaperone, thioredoxin-like protein AAC73594.2

RESULTS_dnaQ

43 ^CHROM ^POS ^{ID REF ALT}

U00096 525637 . CT C

frameshift_variant HIGH rhsD b0497 transcript AAC73599.1 Coding 1/1 c.2378delT p.Leu793fs 2378/4281 2378/4281 793/1426 U00096 gene 523261-

527541

+ rhsD b0497 JW0486 EcoGene:EG10849

U00096 CDS 523261- 527541

+ rhsD b0497 JW0486 EcoGene:EG10849 rhsD protein in rhs element 1 11 Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor AAC73599.1

RESULTS_dnaQ

44 ^CHROM ^POS ^{ID REF ALT}

U00096 525638 . T C,G

C missense_variant MODERATE rhsD b0497 transcript AAC73599.1 Coding 1/1 c.2378T>C p.Leu793Pro 2378/4281 2378/4281 793/1426 G missense_variant MODERATE rhsD b0497 transcript AAC73599.1 Coding 1/1 c.2378T>G p.Leu793Arg 2378/4281 2378/4281 793/1426

U00096 gene 523261- 527541

+ rhsD b0497 JW0486 EcoGene:EG10849

U00096 CDS 523261- 527541

+ rhsD b0497 JW0486 EcoGene:EG10849 rhsD protein in rhs element 1 11 Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor AAC73599.1

RESULTS_dnaQ

RESULTS_CIQ1G 96.3 . 8 1 2 0,0,2,6 58 -42 1.665987e-03 GT:PL:GQ 1/1:204,90,75,131,0,122:27

45 ^CHROM ^POS ^ID ^REF ^ALT

U00096 527613 . ATTTTTT ATTTTTTT

(10)

T frameshift_variant HIGH ybbC b0498 transcript AAC73600.1 Coding 1/1 c.39dupT p.Ile14fs 40/369 40/369 14/122

T downstream_gene_variant MODIFIER rhsD b0497 transcript AAC73599.1 Coding c.*4281dupT 79

U00096 gene 527581-527949 + ybbC b0498 JW0487 EcoGene:EG11769

U00096 CDS 527581-527949 + ybbC b0498 JW0487 EcoGene:EG11769 1 11 putative immunity protein AAC73600.1

RESULTS_dnaQ

46 ^CHROM ^POS ^{ID REF ALT}

U00096 537409 . A C

C missense_variant MODERATE glxR b0509 transcript AAC73611.1 Coding 1/1 c.824A>C p.Asp275Ala 824/879 824/879 275/292 U00096 gene 536586-

537464

+ glxR b0509 ybbQ EcoGene:EG13265

U00096 CDS 536586- 537464

+ glxR b0509 ybbQ EcoGene:EG13265 putative enzyme; Not classified GO_process: GO:0016052 - carbohydrate catabolic process; GO_process: GO:0009441 - glycolate metabolic process; GO_process: GO:0009442 - allantoin assimilation pathway 1 11 tartronate semialdehyde reductase, NADH-dependent AAC73611.1 1.1.1.60

RESULTS_dnaQ

47 ^CHROM ^POS ^{ID REF ALT}

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

48 ^CHROM ^POS ^{ID REF ALT}

U00096 559088 . G A

A missense_variant MODERATE sfmC b0531 transcript AAC73633.1 Coding 1/1 c.115G>A p.Asp39Asn 115/693 115/693 39/230 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

49 ^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

50 ^CHROM ^POS ^ID ^REF ^ALT

U00096 571849 . TAAAA TAAA

(11)

frameshift_variant HIGH ybcM b0546 transcript AAC73647.1 Coding 1/1 c.400delA p.Ile134fs 400/798 400/798 134/265 U00096 gene 571454-

572251

+ ybcM b0546 JW0534 EcoGene:EG13629

U00096 CDS 571454- 572251

+ ybcM b0546 JW0534 EcoGene:EG13629 Phage or Prophage Related putative ARAC-type regulatory protein 1 11 DLP12 prophage; putative DNA-binding transcriptional regulator AAC73647.1

RESULTS_dnaQ

51 ^CHROM ^POS ^{ID REF ALT}

U00096 600325 . A G

G missense_variant MODERATE cusA b0575 transcript AAC73676.1 Coding 1/1 c.1612A>G p.Thr538Ala 1612/3144 1612/3144 538/1047 U00096 gene 598714-

601857

+ cusA b0575 ybdE EcoGene:EG12367

U00096 CDS 598714- 601857

+ cusA b0575 ybdE EcoGene:EG12367 putative transport; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 copper/silver efflux system, membrane component AAC73676.1

RESULTS_dnaQ

52 ^CHROM ^POS ^{ID REF ALT}

U00096 610876 . C T

T missense_variant MODERATE fepA b0584 transcript AAC73685.1 Coding 1/1 c.1619G>A p.Arg540His 1619/2241 1619/2241 540/746 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

53 ^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

54 ^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

(12)

55 ^CHROM U00096 698220 . ^POS ^{ID REF ALT} C T

T missense_variant MODERATE asnB b0674 transcript AAC73768.1 Coding 1/1 c.958G>A p.Asp320Asn 958/1665 958/1665 320/554 U00096 gene 697513-

699177

- asnB b0674 JW0660 EcoGene:EG10092

U00096 CDS 697513- 699177

- asnB b0674 JW0660 EcoGene:EG10092 enzyme; Amino acid biosynthesis: Asparagine GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009063 - cellular amino acid catabolic process; GO_process: GO:0006529 - asparagine biosynthetic process 1 11 asparagine synthetase B AAC73768.1 6.3.5.4

RESULTS_dnaQ

56 ^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

57 ^CHROM ^POS ^{ID REF ALT}

U00096 721882 . C A

A missense_variant MODERATE kdpD b0695 transcript AAC73789.1 Coding 1/1 c.2533G>T p.Val845Leu 2533/2685 2533/2685 845/894

A upstream_gene_variant MODIFIER kdpE b0694 transcript AAC73788.1 Coding c.-1G>T 149

U00096 gene 721730- 724414

U00096 CDS 721730- 724414

RESULTS_dnaQ

RESULTS_CIQ1G 56.0 . 5 -1.291774e+00 0.5 1 1,1,1,2 60 30 1,0.39,1,0.0042 2.309944e-02 GT:PL:GQ 0/1:86,0,57:60

58 ^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

RESULTS_dnaQ

59 ^CHROM ^POS ^{ID REF ALT}

U00096 728332 . GTT GT

frameshift_variant HIGH kdpA b0698 transcript AAC73792.1 Coding 1/1 c.399delA p.Leu133fs 399/1674 399/1674 133/557 U00096 gene 727059-

728732

- kdpA b0698 kac EcoGene:EG10513

U00096 CDS 727059- 728732

- kdpA b0698 kac EcoGene:EG10513 enzyme; Transport of small molecules: Cations ATPase of high-affinity potassium transport system, A chain; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 -

(13)

organelle inner membrane; GO_function: GO:0015662 - ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 1 11 potassium translocating ATPase, subunit A AAC73792.1 3.6.3.12

RESULTS_dnaQ

60 ^CHROM ^POS ^{ID REF ALT}

U00096 736194 . A G

G missense_variant MODERATE ybfC b0704 transcript AAC73798.1 Coding 1/1 c.545A>G p.Glu182Gly 545/570 545/570 182/189

U00096 gene 735650-736219 + ybfC b0704 JW0693 EcoGene:EG11523

U00096 CDS 735650-736219 + ybfC b0704 JW0693 EcoGene:EG11523 1 11 putative secreted protein AAC73798.1

RESULTS_dnaQ

61 ^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

62 ^CHROM ^POS ^{ID REF ALT}

U00096 750915 . C T

T missense_variant MODERATE ybgQ b0718 transcript AAC73812.2 Coding 1/1 c.1255G>A p.Asp419Asn 1255/2448 1255/2448 419/815 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

63 ^CHROM ^POS ^ID ^REF ^ALT

U00096 752776 . GTTTTTT GTTTTT

frameshift_variant HIGH ybgD b0719 transcript AAC73813.1 Coding 1/1 c.14delA p.Gln5fs 14/567 14/567 5/188 U00096 gene 752229-

752795

- ybgD b0719 JW0709 EcoGene:EG12359

U00096 CDS 752229- 752795

- ybgD b0719 JW0709 EcoGene:EG12359 putative structural component; Surface structures putative fimbrial-like protein;

RESULTS_dnaQ

64 ^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

(14)

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

RESULTS_CIQ1G 222.0 . 28 -3.713907e-01 1 2 1,0,14,13 60 -73 1,0.39,1,0.088 1.191301e-01 GT:PL:GQ 1/1:255,46,0:89

65 ^CHROM ^POS ^{ID REF ALT}

U00096 785304 . T C

C missense_variant MODERATE ybgS b0753 transcript AAC73840.1 Coding 1/1 c.14A>G p.Lys5Arg 14/381 14/381 5/126 U00096 gene 784937-

785317

- ybgS b0753 JW0736 EcoGene:EG13663

U00096 CDS 784937- 785317

- ybgS b0753 JW0736 EcoGene:EG13663 putative regulator; Not classified putative homeobox protein 1 11 putative periplasmic protein AAC73840.1

RESULTS_dnaQ

66 ^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

RESULTS_CIQ1G 75.5 . 23 1 2 0,1,11,9 60 -82.5 0.48,1,1,0.18 2.001802e-01 19,0.826087 GT:PL:GQ 1/1:116,48,0:93

67 ^CHROM ^POS ^{ID REF ALT}

U00096 822565 . G A

A missense_variant MODERATE clsB b0789 transcript AAC73876.1 Coding 1/1 c.1175C>T p.Pro392Leu 1175/1242 1175/1242 392/413

A upstream_gene_variant MODIFIER ybhN b0788 transcript AAC73875.1 Coding c.-1C>T 67

U00096 gene 822498- 823739

- clsB b0789 ybhO EcoGene:EG13671

U00096 CDS 822498- 823739

- clsB b0789 ybhO EcoGene:EG13671 Enzyme; Macromolecule synthesis: Phospholipids cardiolipin synthase activity;

GO_process: GO:0008654 - phospholipid biosynthetic process 1 11 cardiolipin synthase 2 AAC73876.1 2.7.8.-

RESULTS_dnaQ

68 ^CHROM ^POS ^ID ^REF ^ALT

U00096 842833 . ATTTTT ATTTT

frameshift_variant HIGH rlmF b0807 transcript AAC73894.2 Coding 1/1 c.507delT p.Phe169fs 507/927 507/927 169/308 U00096 gene 842332-

843258

+ rlmF b0807 ybiN EcoGene:EG13319

U00096 CDS 842332- 843258

+ rlmF b0807 ybiN EcoGene:EG13319 enzyme; rRNA modification 1 11 23S rRNA m(6)A1618 methyltransferase, SAM- dependent AAC73894.2

RESULTS_dnaQ

69 ^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

(15)

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

70 ^CHROM ^POS ^{ID REF ALT}

U00096 868415 . C G

G missense_variant MODERATE gsiA b0829 transcript AAC73916.2 Coding 1/1 c.896C>G p.Ala299Gly 896/1872 896/1872 299/623 U00096 gene 867520-

869391

U00096 CDS 867520- 869391

RESULTS_dnaQ

71 ^CHROM ^POS ^{ID REF ALT}

U00096 868871 . G C

C missense_variant MODERATE gsiA b0829 transcript AAC73916.2 Coding 1/1 c.1352G>C p.Gly451Ala 1352/1872 1352/1872 451/623 U00096 gene 867520-

869391

U00096 CDS 867520- 869391

RESULTS_dnaQ

72 ^CHROM ^POS ^{ID REF ALT}

U00096 871256 . C T

T missense_variant MODERATE gsiC b0831 transcript AAC73918.1 Coding 1/1 c.290C>T p.Pro97Leu 290/921 290/921 97/306 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_dnaQ

73 ^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

74 ^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

(16)

75 ^CHROM ^POS ^{ID REF ALT}

U00096 886780 . A G

G missense_variant MODERATE ybjJ b0845 transcript AAC73932.1 Coding 1/1 c.560T>C p.Ile187Thr 560/1209 560/1209 187/402 U00096 gene 886131-

887339

- ybjJ b0845 JW0829 EcoGene:EG13679

U00096 CDS 886131- 887339

- ybjJ b0845 JW0829 EcoGene:EG13679 putative regulator; Not classified putative DEOR-type transcriptional regulator 1 11 putative drug efflux MFS transporter, inner membrane protein AAC73932.1

RESULTS_dnaQ

76 ^CHROM ^POS ^{ID REF ALT}

U00096 907393 . T C

C missense_variant MODERATE ybjT b0869 transcript AAC73956.2 Coding 1/1 c.890A>G p.Glu297Gly 890/1431 890/1431 297/476 U00096 gene 906852-

908282

- ybjT b0869 JW5116 EcoGene:EG13689

U00096 CDS 906852- 908282

- ybjT b0869 JW5116 EcoGene:EG13689 putative enzyme; Not classified 1 11 putative NAD-dependent oxidoreductase AAC73956.2

RESULTS_dnaQ

77 ^CHROM ^POS ^{ID REF ALT}

U00096 918558 . C A

A missense_variant MODERATE ybjX b0877 transcript AAC73964.1 Coding 1/1 c.563G>T p.Cys188Phe 563/993 563/993 188/330 U00096 gene 918128-

919120

- ybjX b0877 JW0861 EcoGene:EG13693

U00096 CDS 918128- 919120

- ybjX b0877 JW0861 EcoGene:EG13693 putative enzyme; Not classified putative enzyme 1 11 DUF535 family protein AAC73964.1

RESULTS_dnaQ

78 ^CHROM ^POS ^{ID REF ALT}

U00096 930073 . G A

A missense_variant MODERATE cydD b0887 transcript AAC73973.1 Coding 1/1 c.890C>T p.Ala297Val 890/1767 890/1767 297/588 U00096 gene 929196-

930962

- cydD b0887 JW0870 EcoGene:EG11405

U00096 CDS 929196- 930962

- cydD b0887 JW0870 EcoGene:EG11405 transport; Not classified ATP-binding component of cytochrome-related transport, Zn sensitive; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 glutathione/cysteine ABC transporter export permease/ATPase AAC73973.1

RESULTS_dnaQ

79 ^CHROM ^POS ^{ID REF ALT}

U00096 941442 . T G

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

RESULTS_CIQ1G 222.0 . 38 -1.823843e-01 1 2 0,1,14,23 60 -103 1,0.36,1,0.21 2.802913e-01 GT:PL:GQ 1/1:255,76,0:99

Non synonimous mutations found in sample: CIQ1G