mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 6,257 | T→C | Q68R (CAG→CGG) | yaaA ← | peroxide stress resistance protein YaaA |
| RA | 41,063 | A→G | V290A (GTG→GCG) | caiT ← | L‑carnitine:gamma‑butyrobetaine antiporter |
| RA | 70,787 | T→C | F134S (TTT→TCT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 83,945 | A→G | intergenic (‑237/‑423) | leuL ← / → leuO | leu operon leader peptide/DNA‑binding transcriptional dual regulator LeuO |
| RA | 86,365 | (G)5→6 | coding (736/1725 nt) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 134,761 | C→T | intergenic (+11/+27) | yacL → / ← speD | UPF0231 family protein YacL/S‑adenosylmethionine decarboxylase proenzyme |
| RA | 136,888 | G→A | F10F (TTC→TTT) | yacC ← | putative lipoprotein YacC |
| RA | 161,235 | C→T | W84* (TGG→TGA) | sfsA ← | putative DNA‑binding transcriptional regulator of maltose metabolism |
| RA | 220,231 | G→A | T233M (ACG→ATG) | metQ ← | L‑methionine/D‑methionine ABC transporter membrane anchored binding protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 268,471 | (C)5→6 | coding (490/864 nt) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 302,507 | A→G | L23L (TTG→CTG) | paoA ← | aldehyde dehydrogenase, Fe‑S subunit |
| RA | 321,292 | (T)7→8 | intergenic (+211/‑316) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 450,072 | C→T | W190* (TGG→TGA) | cyoB ← | cytochrome bo3 ubiquinol oxidase subunit 1 |
| RA | 499,167 | A→G | R269R (CGT→CGC) | aes ← | acetylesterase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 527,619 | (T)6→5 | coding (39/369 nt) | ybbC → | PF15631 family protein YbbC |
| RA | 668,817 | T→C | S74G (AGC→GGC) | rsfS ← | ribosomal silencing factor RsfS |
| RA | 809,220 | A→G | I13T (ATC→ACC) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 818,656 | G→A | R29R (CGG→CGA) | moaC → | cyclic pyranopterin monophosphate synthase |
| RA | 834,668 | (A)6→7 | coding (1599/2151 nt) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 912,550 | A→G | V422A (GTG→GCG) | hcp ← | protein S‑nitrosylase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 951,191 | (A)6→5 | intergenic (‑111/+81) | pflA ← / ← pflB | pyruvate formate‑lyase activating enzyme/pyruvate formate‑lyase |
| RA | 958,726 | A→G | E358E (GAA→GAG) | serC → | phosphoserine/phosphohydroxythreonine aminotransferase |
| RA | 1,007,546 | C→T | G19S (GGT→AGT) | ycbX ← | 6‑N‑hydroxylaminopurine resistance protein |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,023,186 | C→T | G233E (GGA→GAA) | yccS ← | putative transporter YccS |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,246,924 | T→C | G151G (GGA→GGG) | treA ← | periplasmic trehalase |
| RA | 1,336,761 | G→A | G311S (GGT→AGT) | acnA → | aconitate hydratase 1 |
| RA | 1,384,133 | (A)5→4 | coding (17/1398 nt) | ycjX → | DUF463 domain‑containing protein YcjX |
| RA | 1,393,439 | T→C | N71N (AAT→AAC) | mppA → | murein tripeptide ABC transporter periplasmic binding protein |
| RA | 1,428,077 | A→G | V217A (GTC→GCC) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,466,276 | T→C | pseudogene (885/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,466,280 | A→C | pseudogene (889/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,466,798 | A→G | pseudogene (1407/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,466,846 | C→G | pseudogene (1455/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,466,858 | T→C | pseudogene (1467/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,527,597 | +G | intergenic (+445/‑293) | yncH → / → rhsE | DUF5445 domain‑containing protein YncH/RhsE protein in rhs element |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,569,333 | A→G | F386S (TTT→TCT) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,868,482 | G→A | G525G (GGG→GGA) | yeaG → | protein kinase YeaG |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,886,915 | A→G | G359G (GGT→GGC) | rnd ← | RNase D |
| RA | 1,933,735 | A→G | G290G (GGT→GGC) | edd ← | phosphogluconate dehydratase |
| RA | 1,963,498 | T→G | Q518P (CAG→CCG) | flhA ← | flagellar biosynthesis protein FlhA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,203,742 | T→C | L1155P (CTG→CCG) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,229,203 | (C)5→4 | intergenic (+138/+235) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,268,513 | C→T | R229C (CGT→TGT) | yeiR → | zinc‑binding GTPase YeiR |
| RA | 2,306,256 | G→A | R167C (CGC→TGC) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,340,476 | T→C | K1232E (AAA→GAA) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,346,534 | A→G | E557G (GAG→GGG) | nrdA → | ribonucleoside‑diphosphate reductase 1 subunit alpha |
| RA | 2,355,067 | G→A | R268H (CGC→CAC) | glpB → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B |
| RA | 2,376,497 | A→G | V108A (GTG→GCG) | menB ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA synthase |
| RA | 2,445,843 | G→A | A181V (GCG→GTG) | mepA ← | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑endopeptidase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| JC JC | 2,487,749 | IS1 (–) +9 bp | coding (3376‑3384/3594 nt) | evgS → | sensory histidine kinase EvgS |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,533,728 | T→C | intergenic (+348/‑36) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,584,434 | G→A | G364G (GGC→GGT) | aegA ← | putative oxidoreductase Fe‑S subunit AegA |
| RA | 2,699,027 | G→A | R90H (CGC→CAC) | yfhH → | putative DNA‑binding transcriptional regulator YfhH |
| RA | 2,768,863 | G→A | A67T (GCC→ACC) | yfjQ → | CP4‑57 prophage; protein YfjQ |
| RA | 2,783,509 | T→C | intergenic (‑205/+129) | pinH ← / ← ypjB | putative invertase fragment/DUF5508 domain‑containing protein YpjB |
| RA | 2,801,641 | T→C | R98R (CGT→CGC) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,910,454 | G→A | R78C (CGC→TGC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,000,875 | (C)5→6 | coding (531/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,020,743 | A→G | A68A (GCA→GCG) | ygfM → | putative oxidoreductase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,104,605 | T→C | V58A (GTG→GCG) | mltC → | membrane‑bound lytic murein transglycosylase C |
| RA | 3,126,460 | A→G | D21D (GAT→GAC) | glcE ← | glycolate dehydrogenase, putative FAD‑binding subunit |
| RA | 3,139,565 | C→T | T280M (ACG→ATG) | yghU → | disulfide reductase/organic hydroperoxide reductase |
| RA | 3,152,295 | T→C | T20T (ACT→ACC) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase |
| RA | 3,156,878 | (C)5→6 | coding (256/828 nt) | dkgA → | methylglyoxal reductase DkgA |
| RA | 3,179,729 | T→C | V45A (GTC→GCC) | ygiA → | putative protein YgiA |
| RA | 3,185,389 | A→G | intergenic (+259/‑25) | ubiK → / → ygiL | ubiquinone biosynthesis accessory factor UbiK/putative fimbrial protein YgiL |
| RA | 3,237,402 | T→C | V31A (GTA→GCA) | ygjR → | putative oxidoreductase YgjR |
| RA | 3,292,994 | G→A | I114I (ATC→ATT) | rsmI ← | 16S rRNA 2'‑O‑ribose C1402 methyltransferase |
| RA | 3,305,310 | T→C | S170G (AGC→GGC) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,449,264 | A→T | I207N (ATC→AAC) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,519,289 | T→C | intergenic (‑225/+176) | aroK ← / ← hofQ | shikimate kinase 1/DNA utilization protein HofQ |
| RA | 3,520,253 | G→A | R151C (CGC→TGC) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,659,951 | A→G | V240V (GTA→GTG) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,661,834 | T→G | L474R (CTG→CGG) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,718,375 | A→G | F224L (TTT→CTT) | yiaF ← | DUF3053 domain‑containing protein YiaF |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,922,961 | G→A | intergenic (‑521/+96) | atpI ← / ← rsmG | ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase |
| RA | 3,988,444 | T→C | Q208R (CAG→CGG) | hemX ← | PF04375 family protein HemX |
| RA | 4,112,313 | A→G | intergenic (‑99/‑2) | yiiQ ← / → yiiR | DUF1454 domain‑containing protein YiiQ/DUF805 domain‑containing protein YiiR |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,344,283 | T→C | L305L (CTT→CTC) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,465,380 | C→T | L267L (CTG→CTA) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,541,175 | (A)7→6 | coding (219/603 nt) | fimB → | regulator for fimA |
| RA | 4,549,002 | C→T | C65C (TGC→TGT) | fimH → | type 1 fimbriae D‑mannose specific adhesin |
| RA | 4,587,702 | A→G | T252A (ACT→GCT) | mrr → | methylated adenine and cytosine restriction protein |
| RA | 4,592,948 | G→C | G431A (GGC→GCC) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1466287 | 1466792 | 506 | 19 [18] | [18] 19 | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424525–3424239 | 6–760 | 19 [18] | [14] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3944039–3944058 | 3946509–3946229 | 2172–2471 | 21 [17] | [18] 19 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 76 (1.050) | 30 (0.470) | 25/244 | 1.3 | 30.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 71 (1.110) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 71 (1.010) | 54/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 106 (1.460) | 136 (1.880) | 67/274 | 0.0 | 72.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 86 (1.180) | 50/276 | 0.3 | 95.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||