Non synonimous mutations found in sample: ΔdnaQ

(1)

Non synonimous mutations found in sample: ΔdnaQ

FILTERS: (ANN contains MODERATE OR HIGH)

1 CHROM POS ID REF ALT U00096 38036 . G T

T missense_variant MODERATE caiB b0038 transcript AAC73149.1 Coding 1/1 c.1080C>A p.Phe360Leu 1080/1218 1080/1218 360/405 U00096 gene 37898-

39115

- caiB b0038 yaaN EcoGene:EG11559

U00096 CDS 37898- 39115

- caiB b0038 yaaN EcoGene:EG11559 enzyme; Central intermediary metabolism: Pool, multipurpose conversions l-carnitine dehydratase; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0042413 - carnitine catabolic process;

GO_process: GO:0009310 - amine catabolic process 1 11 crotonobetainyl CoA:carnitine CoA transferase AAC73149.1 2.8.3.- N-terminus verified by Edman degradation: PMID 8188598,10209289

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

RESULTS_dnaQ 226.0 . 23 3.818813e-01 0.7304 1 0,2,10,11 60 -25 0.49,0.3,1,0.14 1.304463e-01 GT:PL:GQ 0/1:255,0,2:5

2 CHROM POS ID REF ALT U00096 79341 . C A

A missense_variant MODERATE leuD b0071 transcript AAC73182.1 Coding 1/1 c.113G>T p.Gly38Val 113/606 113/606 38/201

A downstream_gene_variant MODIFIER leuC b0072 transcript AAC73183.1 Coding c.*1401G>T 123

U00096 gene 78848- 79453

- leuD b0071 JW0070 EcoGene:EG11575 U00096 CDS 78848-

79453

- leuD b0071 JW0070 EcoGene:EG11575 enzyme; Amino acid biosynthesis: Leucine isopropylmalate isomerase subunit;

GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009098 - leucine biosynthetic process 1 11 3-isopropylmalate dehydratase small subunit AAC73182.1 4.2.1.33

RESULTS_dnaQ 222.0 . 33 1 2 0,0,13,20 59 -126 2.805656e-01 GT:PL:GQ 1/1:255,99,0:99

3 CHROM POS ID REF ALT U00096 91323 . G A

A missense_variant MODERATE ftsL b0083 transcript AAC73194.1 Coding 1/1 c.292G>A p.Glu98Lys 292/366 292/366 98/121

A upstream_gene_variant MODIFIER ftsI b0084 transcript AAC73195.1 Coding c.-1G>A 90

U00096 gene 91032- 91397

+ ftsL b0083 yabD EcoGene:EG11086 U00096 CDS 91032-

91397

+ ftsL b0083 yabD EcoGene:EG11086 phenotype; Cell division cell division protein; ingrowth of wall at septum 1 11 membrane bound cell division leucine zipper septum protein AAC73194.1

4 ^CHROM ^POS ^{ID REF ALT}

U00096 104426 . C T

T missense_variant MODERATE ftsA b0094 transcript AAC73205.1 Coding 1/1 c.445C>T p.Leu149Phe 445/1263 445/1263 149/420 U00096 gene 103982-

105244

+ ftsA b0094 JW0092 EcoGene:EG10339

U00096 CDS 103982- 105244

+ ftsA b0094 JW0092 EcoGene:EG10339 phenotype; Cell division ATP-binding cell division protein, septation process, complexes with FtsZ, associated with junctions of inner and outer membranes; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 ATP-binding cell division FtsK recruitment protein AAC73205.1

5 ^CHROM ^POS ^{ID REF ALT}

U00096 191485 . A G

(2)

G missense_variant MODERATE tsf b0170 transcript AAC73281.1 Coding 1/1 c.629A>G p.Glu210Gly 629/852 629/852 210/283 U00096 gene 190857-

191708

+ tsf b0170 JW0165 EcoGene:EG11033

U00096 CDS 190857- 191708

+ tsf b0170 JW0165 EcoGene:EG11033 factor; Proteins - translation and modification GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006412 - translation 1 11 translation elongation factor EF-Ts AAC73281.1

6 ^CHROM ^POS ^{ID REF ALT}

U00096 208192 . T A

A missense_variant MODERATE dnaE b0184 transcript AAC73295.1 Coding 1/1 c.3067T>A p.Ser1023Thr 3067/3483 3067/3483 1023/1160 U00096 gene 205126-

208608

+ dnaE b0184 sdgC EcoGene:EG10238 U00096 CDS 205126-

208608

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

7 ^CHROM ^POS ^{ID REF ALT}

U00096 236775 . G A

A missense_variant MODERATE dnaQ b0215 transcript AAC73320.1 Coding 1/1 c.709G>A p.Gly237Arg 709/732 709/732 237/243 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

8 ^CHROM ^POS ^{ID REF ALT}

U00096 236776 . G C

C missense_variant MODERATE dnaQ b0215 transcript AAC73320.1 Coding 1/1 c.710G>C p.Gly237Ala 710/732 710/732 237/243 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

9 ^CHROM ^POS ^{ID REF ALT}

U00096 258675 . C G

G splice_acceptor_variant&intron_variant HIGH crl b0240 transcript b0240 Coding 1/1 c.72-1C>G U00096 gene 257829-

257899,258676- 259006

+ crl b0240 JW0230 EcoGene:EG11092

U00096 CDS 257829- 257899,258676- 259006

+ crl b0240 JW0230 EcoGene:EG11092 pseudogene, sigma factor-binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers; GO_component: GO:0009289 - pilus; GO_component: GO:0005737 - cytoplasm; GO_function:

GO:0016563 - transcription activator activity; GO_process: GO:0006350 - transcription 1 11

RESULTS_dnaQ 3.07 . 2 -9.668049e-01 1 2 0,1,1,0 42 -28 1,1,1,1 GT:PL:GQ 0/1:29,1,0:6

(3)

10 ^CHROM ^POS ^{ID REF ALT}

U00096 304754 . C T

T missense_variant MODERATE ecpE b0289 transcript AAC73392.2 Coding 1/1 c.452G>A p.Arg151Gln 452/711 452/711 151/236 U00096 gene 304495-305205 - ecpE b0289 yagV EcoGene:EG13561

U00096 CDS 304495-305205 - ecpE b0289 yagV EcoGene:EG13561 factor; Surface structures 1 11 ECP production pilus chaperone AAC73392.2

11 ^CHROM ^POS ^{ID REF ALT}

U00096 314731 . TAAA TAA

frameshift_variant HIGH eaeH b0297 transcript b0297 Coding 1/1 c.378delA p.Lys126fs 378/872 378/872 126/289 WARNING_TRANSCRIPT_INCOMPLETE 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 214.0 . 26 1 2 0,0,10,15 60 -110 2.033918e-01 24,0.923077 GT:PL:GQ 1/1:255,75,0:99

12 ^CHROM ^POS ^{ID REF ALT}

U00096 334105 . T G

G missense_variant MODERATE yahB b0316 transcript AAC73419.1 Coding 1/1 c.329A>C p.His110Pro 329/933 329/933 110/310 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

13 ^CHROM ^POS ^{ID REF ALT}

U00096 341434 . C G

G missense_variant MODERATE yahJ b0324 transcript AAC73427.1 Coding 1/1 c.310C>G p.Pro104Ala 310/1383 310/1383 104/460 U00096 gene 341125-

342507

+ yahJ b0324 JW0316 EcoGene:EG13594

U00096 CDS 341125- 342507

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

14 ^CHROM ^POS ^{ID REF ALT}

U00096 508288 . A G

G missense_variant MODERATE ybaQ b0483 transcript AAC73585.2 Coding 1/1 c.71A>G p.Asp24Gly 71/342 71/342 24/113

U00096 gene 508218-508559 + ybaQ b0483 JW0472 EcoGene:EG13245

U00096 CDS 508218-508559 + ybaQ b0483 JW0472 EcoGene:EG13245 1 11 putative DNA-binding transcriptional regulator AAC73585.2

15 ^CHROM ^POS ^{ID REF ALT}

U00096 538029 . A G

(4)

G missense_variant MODERATE ybbW b0511 transcript AAC73613.2 Coding 1/1 c.397A>G p.Ile133Val 397/1455 397/1455 133/484 U00096 gene 537633-

539087

+ ybbW b0511 JW0499 EcoGene:EG13618

U00096 CDS 537633- 539087

+ ybbW b0511 JW0499 EcoGene:EG13618 putative transport; Transport of small molecules: Carbohydrates, organic acids, alcohols GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 putative allantoin transporter AAC73613.2

16 ^CHROM ^POS ^{ID REF ALT}

U00096 698541 . G T

T missense_variant MODERATE asnB b0674 transcript AAC73768.1 Coding 1/1 c.637C>A p.Arg213Ser 637/1665 637/1665 213/554 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

17 ^CHROM ^POS ^{ID REF ALT}

U00096 922079 . T G

G missense_variant MODERATE macB b0879 transcript AAC73966.1 Coding 1/1 c.1733T>G p.Leu578Arg 1733/1947 1733/1947 578/648 U00096 gene 920347-

922293

+ macB b0879 ybjZ EcoGene:EG13695 U00096 CDS 920347-

922293

+ macB b0879 ybjZ EcoGene:EG13695 putative transport; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 macrolide ABC transporter

peremase/ATPase AAC73966.1

18 ^CHROM ^POS ^{ID REF ALT}

U00096 1064853 . A T

T missense_variant MODERATE yccE b1001 transcript AAC74086.1 Coding 1/1 c.818A>T p.Asp273Val 818/1257 818/1257 273/418

U00096 gene 1064036-1065292 + yccE b1001 JW0986 EcoGene:EG12196

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

19 ^CHROM ^POS ^{ID REF ALT}

U00096 1096234 . C G

G missense_variant MODERATE ycdU b1029 transcript AAC74114.1 Coding 1/1 c.392C>G p.Pro131Arg 392/987 392/987 131/328

U00096 gene 1095843-1096829 + ycdU b1029 JW1015 EcoGene:EG13867

U00096 CDS 1095843-1096829 + ycdU b1029 JW1015 EcoGene:EG13867 1 11 putative inner membrane protein AAC74114.1

20 ^CHROM ^POS ^{ID REF ALT}

U00096 1104203 . A G

G missense_variant MODERATE csgB b1041 transcript AAC74125.1 Coding 1/1 c.253A>G p.Thr85Ala 253/456 253/456 85/151 U00096 gene 1103951- + csgB b1041 JW1024 EcoGene:EG12621

(5)

1104406 U00096 CDS 1103951-

1104406

+ csgB b1041 JW1024 EcoGene:EG12621 structural component; Surface structures minor curlin subunit precursor, similar ro CsgA; GO_component: GO:0009289 - pilus; GO_component: GO:0009279 - cell outer membrane; GO_process:

GO:0009101 - glycoprotein biosynthetic process 1 11 curlin nucleator protein, minor subunit in curli complex AAC74125.1

21 ^CHROM ^POS ^{ID REF ALT}

U00096 1284681 . T C

C missense_variant MODERATE narH b1225 transcript AAC74309.1 Coding 1/1 c.1078T>C p.Ser360Pro 1078/1539 1078/1539 360/512 U00096 gene 1283604-

1285142

+ narH b1225 JW1216 EcoGene:EG10639 U00096 CDS 1283604-

1285142

+ narH b1225 JW1216 EcoGene:EG10639 enzyme; Energy metabolism, carbon: Anaerobic respiration nitrate reductase 1, beta subunit; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009061 - anaerobic respiration 1 11 nitrate reductase 1, beta (Fe-S) subunit AAC74309.1 1.7.99.4 N-terminus verified by Edman degradation: PMID 3053688

22 ^CHROM ^POS ^{ID REF ALT}

U00096 1428030 . C G

G missense_variant MODERATE insH1 b1370 transcript AAC74452.1 Coding 1/1 c.697G>C p.Ala233Pro 697/981 697/981 233/326

G intron_variant MODIFIER lomR b4570 transcript b4570 Coding 1/1 c.210+432C>G WARNING_TRANSCRIPT_NO_START_CODON U00096 gene 1427746-

1428726

- insH1 b1370 ECK0261 EcoGene:EG40008 U00096 CDS 1427746-

1428726

- insH1 b1370 ECK0261 EcoGene:EG40008 IS, phage, Tn; Transposon-related functions; extrachromosomal;

transposon related 1 11 IS5 transposase and trans-activator AAC74452.1

23 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1490949 . CTTTTT CTTTT

frameshift_variant HIGH cybB b1418 transcript AAC74500.2 Coding 1/1 c.53delT p.Leu18fs 53/531 53/531 18/176 U00096 gene 1490902-

1491432

+ cybB b1418 JW5224 EcoGene:EG10172 U00096 CDS 1490902-

1491432

+ cybB b1418 JW5224 EcoGene:EG10172 enzyme; Energy metabolism, carbon: Electron transport GO_function:

GO:0009055 - electron carrier activity; GO_process: GO:0017004 - cytochrome complex assembly 1 11 cytochrome b561 AAC74500.2

RESULTS_dnaQ 80.5 . 11 1 2 0,0,6,3 60 -61.5 1.286459e-01 9,0.818182 GT:PL:GQ 1/1:121,27,0:51

24 ^CHROM ^POS ^{ID REF ALT}

U00096 1497760 . A C

C missense_variant MODERATE opgD b1424 transcript AAC74506.3 Coding 1/1 c.905A>C p.Asp302Ala 905/1656 905/1656 302/551 U00096 gene 1496856-

1498511

+ opgD b1424 yzzZ EcoGene:EG12859 U00096 CDS 1496856-

1498511

+ opgD b1424 yzzZ EcoGene:EG12859 putative structure; Not classified putative glycoprotein; GO_component:

GO:0042597 - periplasmic space; GO_process: GO:0006970 - response to osmotic stress 1 11 OPG biosynthetic periplasmic protein AAC74506.3

25 ^CHROM ^POS ^{ID REF ALT}

U00096 1512246 . T G

(6)

G missense_variant MODERATE ydcS b1440 transcript AAC74522.1 Coding 1/1 c.593T>G p.Val198Gly 593/1146 593/1146 198/381 U00096 gene 1511654-

1512799

+ ydcS b1440 JW1435 EcoGene:EG13762 U00096 CDS 1511654-

1512799

+ ydcS b1440 JW1435 EcoGene:EG13762 enzyme; Not classified periplasmic-binding component of ABC superfamily;

GO_component: GO:0042597 - periplasmic space 1 11 putative ABC transporter periplasmic binding protein AAC74522.1

26 ^CHROM ^POS ^{ID REF ALT}

U00096 1520982 . A G

G missense_variant MODERATE yncD b1451 transcript AAC74533.1 Coding 1/1 c.2084T>C p.Ile695Thr 2084/2103 2084/2103 695/700

G downstream_gene_variant MODIFIER mcbR b1450 transcript AAC74532.2 Coding c.*666A>G 55

U00096 gene 1520963- 1523065

- yncD b1451 JW1446 EcoGene:EG13774 U00096 CDS 1520963-

1523065

- yncD b1451 JW1446 EcoGene:EG13774 putative transport; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative iron outer membrane transporter AAC74533.1

27 ^CHROM ^POS ^{ID REF ALT}

U00096 1575336 . T G

G missense_variant MODERATE yddB b1495 transcript AAC74568.1 Coding 1/1 c.2284A>C p.Ser762Arg 2284/2373 2284/2373 762/790

G upstream_gene_variant MODIFIER pqqL b1494 transcript AAC74567.1 Coding c.-1A>C 134

U00096 gene 1575247-1577619 - yddB b1495 JW1490 EcoGene:EG11743

U00096 CDS 1575247-1577619 - yddB b1495 JW1490 EcoGene:EG11743 1 11 putative TonB-dependent outer membrane receptor AAC74568.1

28 ^CHROM ^POS ^{ID REF ALT}

U00096 1578871 . A G

G missense_variant MODERATE yddA b1496 transcript AAC74569.1 Coding 1/1 c.472T>C p.Phe158Leu 472/1686 472/1686 158/561 U00096 gene 1577657-

1579342

- yddA b1496 JW5242 EcoGene:EG11742 U00096 CDS 1577657-

1579342

- yddA b1496 JW5242 EcoGene:EG11742 putative transport; Not classified GO_component: GO:0009274 - peptidoglycan- based cell wall; GO_component: GO:0019866 - organelle inner membrane 1 11 putative multidrug ABC transporter permease/ATPase AAC74569.1

29 ^CHROM ^POS ^{ID REF ALT}

U00096 1610589 . A G

G missense_variant MODERATE uxaB b1521 transcript AAT48131.1 Coding 1/1 c.92T>C p.Val31Ala 92/1452 92/1452 31/483 U00096 gene 1609229-

1610680

- uxaB b1521 JW1514 EcoGene:EG11065 U00096 CDS 1609229-

1610680

- uxaB b1521 JW1514 EcoGene:EG11065 enzyme; Degradation of small molecules: Carbon compounds altronate oxidoreductase; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 altronate oxidoreductase, NAD- dependent AAT48131.1 1.1.1.58 N-terminus verified by Edman degradation: PMID 3525742

30 ^CHROM ^POS ^{ID REF ALT}

(7)

U00096 1658706 . G C

C missense_variant MODERATE ynfE b1587 transcript AAC74659.1 Coding 1/1 c.638G>C p.Gly213Ala 638/2427 638/2427 213/808 U00096 gene 1658069-

1660495

+ ynfE b1587 JW1579 EcoGene:EG13843 U00096 CDS 1658069-

1660495

+ ynfE b1587 JW1579 EcoGene:EG13843 putative enzyme; Not classified 1 11 putative selenate reductase, periplasmic AAC74659.1

31 ^CHROM ^POS ^{ID REF ALT}

U00096 1706464 . A T

T missense_variant MODERATE rsxB b1628 transcript AAC74700.1 Coding 1/1 c.117A>T p.Lys39Asn 117/579 117/579 39/192

T downstream_gene_variant MODIFIER rsxA b1627 transcript AAC74699.1 Coding c.*582A>T 116

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

32 ^CHROM ^POS ^{ID REF ALT}

U00096 1750974 . T A

A missense_variant MODERATE ydhX b1671 transcript AAC74741.4 Coding 1/1 c.40A>T p.Thr14Ser 40/669 40/669 14/222

A downstream_gene_variant MODIFIER ydhW b1672 transcript AAC74742.1 Coding c.*648A>T 103

U00096 gene 1750345- 1751013

- ydhX b1671 JW5271 EcoGene:EG13958 U00096 CDS 1750345-

1751013

- ydhX b1671 JW5271 EcoGene:EG13958 putative enzyme; Not classified putative oxidoreductase, Fe-S subunit 1 11 putative 4Fe-4S ferridoxin-type protein; FNR, Nar, NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex AAC74741.4

33 ^CHROM ^POS ^{ID REF ALT}

U00096 1774321 . T C

C missense_variant MODERATE ydiB b1692 transcript AAC74762.1 Coding 1/1 c.533T>C p.Val178Ala 533/867 533/867 178/288 U00096 gene 1773789-

1774655

+ ydiB b1692 JW1682 EcoGene:EG11234

U00096 CDS 1773789- 1774655

+ ydiB b1692 JW1682 EcoGene:EG11234 putative enzyme; Not classified putative oxidoreductase 1 11 quinate/shikimate 5-dehydrogenase, NAD(P)-binding AAC74762.1 1.1.1.25

34 ^CHROM ^POS ^{ID REF ALT}

U00096 1796866 . T C

C missense_variant MODERATE pheT b1713 transcript AAC74783.1 Coding 1/1 c.1079A>G p.Tyr360Cys 1079/2388 1079/2388 360/795 U00096 gene 1795557-

1797944

- pheT b1713 JW1703 EcoGene:EG10710 U00096 CDS 1795557-

1797944

- pheT b1713 JW1703 EcoGene:EG10710 enzyme; Aminoacyl tRNA synthetases, tRNA modification phenylalanine tRNA synthetase, beta-subunit; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006418 - tRNA aminoacylation for protein translation 1 11 phenylalanine tRNA synthetase, beta subunit AAC74783.1 6.1.1.20

(8)

35 ^CHROM U00096 1830943 . ^POS ^{ID REF ALT} T C

C missense_variant MODERATE astC b1748 transcript AAC74818.1 Coding 1/1 c.1040A>G p.Tyr347Cys 1040/1221 1040/1221 347/406

C upstream_gene_variant MODIFIER astA b1747 transcript AAC74817.1 Coding c.-1A>G 178

U00096 gene 1830762- 1831982

- astC b1748 ydjW EcoGene:EG13999 U00096 CDS 1830762-

1831982

- astC b1748 ydjW EcoGene:EG13999 enzyme; Amino acid biosynthesis: Arginine acetylornithine delta-aminotransferase;

GO_process: GO:0009063 - cellular amino acid catabolic process 1 11 succinylornithine transaminase, PLP-dependent AAC74818.1 2.6.1.17

36 ^CHROM ^POS ^{ID REF ALT}

U00096 1832618 . G C

C missense_variant MODERATE xthA b1749 transcript AAC74819.1 Coding 1/1 c.191G>C p.Gly64Ala 191/807 191/807 64/268 U00096 gene 1832428-

1833234

+ xthA b1749 xth EcoGene:EG11073 U00096 CDS 1832428-

1833234

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

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

37 ^CHROM ^POS ^ID ^REF ^ALT

U00096 1915171 . GTTTTTT GTTTTT

frameshift_variant HIGH proQ b1831 transcript AAC74901.2 Coding 1/1 c.358delA p.Lys120fs 358/699 358/699 120/232 U00096 gene 1914836-

1915534

- proQ b1831 yoeC EcoGene:EG12866 U00096 CDS 1914836-

1915534

- proQ b1831 yoeC EcoGene:EG12866 regulator of ProP; putative structural element which influences activation of ProP;

GO_process: GO:0006970 - response to osmotic stress 1 11 RNA chaperone, putative ProP translation regulator AAC74901.2

38 ^CHROM ^POS ^{ID REF ALT}

U00096 2015409 . A G

G missense_variant MODERATE fliG b1939 transcript AAC75006.1 Coding 1/1 c.530A>G p.Glu177Gly 530/996 530/996 177/331 U00096 gene 2014880-

2015875

+ fliG b1939 JW1923 EcoGene:EG11654 U00096 CDS 2014880-

2015875

+ fliG b1939 JW1923 EcoGene:EG11654 structural component; Surface structures flagellar biosynthesis, component of motor switching and energizing, enabling rotation and determining its direction; GO_component: GO:0019861 - flagellum;

GO_process: GO:0009296 - flagellum assembly; GO_process: GO:0042330 - taxis 1 11 flagellar motor switching and energizing component AAC75006.1

39 ^CHROM ^POS ^ID ^REF ^ALT

U00096 2150628 . GAAAA GAAA

frameshift_variant HIGH yegI b2070 transcript AAC75131.1 Coding 1/1 c.354delT p.Asp118fs 354/1947 354/1947 118/648 U00096 gene 2149039-

2150985

- yegI b2070 JW2055 EcoGene:EG14052 U00096 CDS 2149039-

2150985

- yegI b2070 JW2055 EcoGene:EG14052 putative enzyme; Not classified putative chaperonin 1 11 protein kinase- related putative non-specific DNA-binding protein AAC75131.1

(9)

40 ^CHROM ^POS ^{ID REF ALT}

U00096 2221701 . T C

C missense_variant MODERATE bglX b2132 transcript AAC75193.1 Coding 1/1 c.289A>G p.Met97Val 289/2298 289/2298 97/765 U00096 gene 2219692-

2221989

- bglX b2132 yohA EcoGene:EG12013 U00096 CDS 2219692-

2221989

- bglX b2132 yohA EcoGene:EG12013 enzyme; Degradation of small molecules: Carbon compounds GO_component:

GO:0042597 - periplasmic space; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 beta-D-glucoside glucohydrolase, periplasmic AAC75193.1 3.2.1.21

41 ^CHROM ^POS ^{ID REF ALT}

U00096 2259134 . T A

A missense_variant MODERATE psuK b2166 transcript AAC75227.1 Coding 1/1 c.163A>T p.Asn55Tyr 163/942 163/942 55/313 U00096 gene 2258355-

2259296

- psuK b2166 yeiC EcoGene:EG11646 U00096 CDS 2258355-

2259296

- psuK b2166 yeiC EcoGene:EG11646 enzyme; pseudouridine utilization putative kinase 1 11 pseudouridine kinase AAC75227.1

42 ^CHROM ^POS ^{ID REF ALT}

U00096 2260779 . T C

C missense_variant MODERATE fruA b2167 transcript AAC75228.1 Coding 1/1 c.632A>G p.Lys211Arg 632/1692 632/1692 211/563 U00096 gene 2259719-

2261410

- fruA b2167 ptsF EcoGene:EG10336 U00096 CDS 2259719-

2261410

- fruA b2167 ptsF EcoGene:EG10336 regulator; Degradation of small molecules: Carbon compounds PTS system, fructose-specific transport protein; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_process: GO:0016052 - carbohydrate catabolic process 1 11 fused fructose-specific PTS enzymes: IIBcomponent/IIC components AAC75228.1

43 ^CHROM ^POS ^ID ^REF ^ALT

U00096 2517362 . GAAAAA GAAAA

frameshift_variant HIGH yfeA b2395 transcript AAC75454.2 Coding 1/1 c.466delT p.Phe156fs 466/2190 466/2190 156/729 U00096 gene 2515643-2517832 - yfeA b2395 JW5391 EcoGene:EG11145

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

44 ^CHROM ^POS ^{ID REF ALT}

U00096 2693373 . G C

C missense_variant MODERATE purL b2557 transcript AAT48143.1 Coding 1/1 c.2171C>G p.Ala724Gly 2171/3888 2171/3888 724/1295 U00096 gene 2691656-

2695543

- purL b2557 purI EcoGene:EG10797

U00096 CDS 2691656- 2695543

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

(10)

45 ^CHROM ^POS ^{ID REF ALT}

U00096 2717817 . C T

T missense_variant MODERATE yfiF b2581 transcript AAC75634.1 Coding 1/1 c.712G>A p.Ala238Thr 712/1038 712/1038 238/345 U00096 gene 2717491-

2718528

- yfiF b2581 JW2565 EcoGene:EG11786 U00096 CDS 2717491-

2718528

- yfiF b2581 JW2565 EcoGene:EG11786 GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009451 - RNA modification 1 11 putative methyltransferase AAC75634.1

46 ^CHROM ^POS ^{ID REF ALT}

U00096 3190185 . T C

C missense_variant MODERATE yqiH b3047 transcript AAC76083.2 Coding 1/1 c.305T>C p.Leu102Pro 305/750 305/750 102/249 U00096 gene 3189881-

3190630

+ yqiH b3047 JW5508 EcoGene:EG14229

U00096 CDS 3189881- 3190630

+ yqiH b3047 JW5508 EcoGene:EG14229 putative factor; Surface structures putative membrane protein; GO_component:

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

GO:0006457 - protein folding 1 11 putative periplasmic pilin chaperone AAC76083.2

47 ^CHROM ^POS ^{ID REF ALT}

U00096 3243047 . A T

T missense_variant MODERATE uxaA b3091 transcript AAC76126.1 Coding 1/1 c.268T>A p.Tyr90Asn 268/1488 268/1488 90/495 U00096 gene 3241827-

3243314

- uxaA b3091 ygjW EcoGene:EG12734 U00096 CDS 3241827-

3243314

- uxaA b3091 ygjW EcoGene:EG12734 enzyme; Degradation of small molecules: Carbon compounds GO_process:

GO:0016052 - carbohydrate catabolic process 1 11 altronate hydrolase AAC76126.1 4.2.1.7

48 ^CHROM ^POS ^{ID REF ALT}

U00096 3362820 . C T

T missense_variant MODERATE yhcD b3216 transcript AAC76248.1 Coding 1/1 c.14C>T p.Thr5Met 14/2382 14/2382 5/793

T downstream_gene_variant MODIFIER yhcA b3215 transcript AAC76247.1 Coding c.*675C>T 34

U00096 gene 3362807- 3365188

+ yhcD b3216 JW3183 EcoGene:EG12810 U00096 CDS 3362807-

3365188

+ yhcD b3216 JW3183 EcoGene:EG12810 putative membrane; Not classified putative outer membrane protein;

GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0009279 - cell outer membrane 1 11 putative outer membrane fimbrial subunit usher protein AAC76248.1

49 ^CHROM ^POS ^{ID REF ALT}

U00096 3795757 . G C

C missense_variant MODERATE waaF b3620 transcript AAC76644.1 Coding 1/1 c.829G>C p.Ala277Pro 829/1047 829/1047 277/348 U00096 gene 3794929-

3795975

+ waaF b3620 rfaF EcoGene:EG12210

U00096 CDS 3794929- 3795975

+ waaF b3620 rfaF EcoGene:EG12210 enzyme; Macromolecule metabolism: Lipopolysaccharide ADP-heptose--lps heptosyltransferase II; lipopolysaccharide core biosynthesis; GO_function: GO:0042280 - cell surface antigen activity,

(11)

host-interacting; GO_process: GO:0009244 - lipopolysaccharide core region biosynthetic process 1 11 ADP-heptose:LPS heptosyltransferase II AAC76644.1 2.-.-.-

50 ^CHROM ^POS ^ID ^REF ^ALT

U00096 3797153 . TAAAAAA TAAAAA

frameshift_variant HIGH waaL b3622 transcript AAC76646.1 Coding 1/1 c.212delA p.Asn71fs 212/1260 212/1260 71/419 U00096 gene 3796948-

3798207

+ waaL b3622 rfaL EcoGene:EG11424 U00096 CDS 3796948-

3798207

+ waaL b3622 rfaL EcoGene:EG11424 enzyme; Macromolecule metabolism: Lipopolysaccharide O-antigen ligase;

lipopolysaccharide core biosynthesis; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component:

GO:0019866 - organelle inner membrane; GO_function: GO:0042280 - cell surface antigen activity, host-interacting;

GO_process: GO:0009244 - lipopolysaccharide core region biosynthetic process 1 11 O-antigen ligase AAC76646.1

RESULTS_dnaQ 31.7 . 7 1 2 0,0,3,2 60 -49.5 8.540571e-02 5,0.714286 GT:PL:GQ 1/1:72,15,0:27

51 ^CHROM ^POS ^ID ^REF ^ALT

U00096 3949776 . ATTTTTTT ATTTTTT

frameshift_variant HIGH yifB b3765 transcript AAC77486.2 Coding 1/1 c.187delA p.Lys63fs 187/1521 187/1521 63/506 U00096 gene 3948449-

3949969

- yifB b3765 JW3738 EcoGene:EG11260

U00096 CDS 3948449- 3949969

- yifB b3765 JW3738 EcoGene:EG11260 putative regulator; Not classified putative 2-component regulator 1 11 magnesium chelatase family protein and putative transcriptional regulator AAC77486.2

52 ^CHROM ^POS ^{ID REF ALT}

U00096 4007952 . A G

G missense_variant MODERATE rhtC b3823 transcript AAT48222.1 Coding 1/1 c.196A>G p.Lys66Glu 196/621 196/621 66/206 U00096 gene 4007757-

4008377

+ rhtC b3823 yigJ EcoGene:EG11468 U00096 CDS 4007757-

4008377

+ rhtC b3823 yigJ EcoGene:EG11468 amino acid exporter (threonine); threonine efflux protein (RhtB family);

GO_component: GO:0019866 - organelle inner membrane; GO_process: GO:0009088 - threonine biosynthetic process 1 11 threonine efflux pump AAT48222.1

53 ^CHROM ^POS ^{ID REF ALT}

U00096 4371109 . G A

A missense_variant MODERATE groL b4143 transcript AAC77103.1 Coding 1/1 c.85G>A p.Val29Ile 85/1647 85/1647 29/548

A downstream_gene_variant MODIFIER groS b4142 transcript AAC77102.1 Coding c.*294G>A 128

U00096 gene 4371025- 4372671

+ groL b4143 mopA EcoGene:EG10599 U00096 CDS 4371025-

4372671

+ groL b4143 mopA EcoGene:EG10599 factor; Chaperones GO_component: GO:0005737 - cytoplasm; GO_process:

GO:0006457 - protein folding 1 11 Cpn60 chaperonin GroEL, large subunit of GroESL AAC77103.1

Non synonimous mutations found in sample: ΔdnaQ