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 | freq | annotation | gene | description |
| RA | 65,508 | A→G | 6.8% | N91N (AAT→AAC) | polB ← | DNA polymerase II |
| RA | 87,944 | T→C | 5.1% | intergenic (+96/‑84) | ilvH → / → cra | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra |
| RA | 122,714 | C→T | 6.4% | A208V (GCG→GTG) | pdhR → | DNA‑binding transcriptional dual regulator PdhR |
| RA | 127,637 | G→T | 16.3% | intergenic (+50/‑275) | aceF → / → lpd | pyruvate dehydrogenase, E2 subunit/lipoamide dehydrogenase |
| RA | 138,373 | C→T | 5.2% | R431C (CGT→TGT) | cueO → | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
| RA | 144,946 | Δ1 bp | 11.8% | coding (370/441 nt) | yadI → | putative PTS enzyme IIA component YadI |
| RA | 144,947 | Δ1 bp | 11.8% | coding (371/441 nt) | yadI → | putative PTS enzyme IIA component YadI |
| RA | 174,213 | G→A | 7.1% | R224C (CGC→TGC) | hemL ← | glutamate‑1‑semialdehyde aminotransferase |
| RA | 174,298 | C→A | 7.0% | P195P (CCG→CCT) | hemL ← | glutamate‑1‑semialdehyde aminotransferase |
| RA | 238,497 | G→T | 16.9% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 18.9% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 20.7% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 24.7% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 20.5% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 23.6% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 288,353 | A→C | 34.6% | D522A (GAC→GCC) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 298,537 | G→C | 18.2% | R64G (CGC→GGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 403,738 | C→A | 16.5% | F12L (TTC→TTA) | dgcC → | diguanylate cyclase DgcC |
| RA | 454,877 | A→T | 25.5% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 464,190 | A→T | 6.0% | Q85L (CAG→CTG) | ybaV → | helix‑hairpin‑helix 3 family protein |
| RA | 476,108 | A→T | 7.9% | N88K (AAT→AAA) | atl ← | DNA base‑flipping protein |
| RA | 583,678 | A→G | 6.1% | intergenic (+618/‑3) | tfaX → / → appY | DLP12 prophage; protein TfaX/DNA‑binding transcriptional activator AppY |
| RA | 623,278 | G→A | 7.0% | V327I (GTC→ATC) | entS → | enterobactin exporter EntS |
| RA | 729,372 | A→C | 39.5% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 729,383 | T→G | 38.7% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 814,863 | C→T | 8.5% | N446N (AAC→AAT) | uvrB → | excision nuclease subunit B |
| RA | 1,016,066 | A→T | 6.4% | V135V (GTT→GTA) | fabA ← | beta‑hydroxyacyl‑acyl carrier protein dehydratase/isomerase |
| RA | 1,059,911 | T→C | 6.1% | L219S (TTG→TCG) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,145,638 | T→C | 7.5% | R233R (CGT→CGC) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,193,663 | C→A | 30.5% | M37I (ATG→ATT) | mnmA ← | tRNA‑specific 2‑thiouridylase |
| RA | 1,260,352 | T→C | 7.8% | Q151R (CAG→CGG) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | 1,297,137 | T→G | 13.1% | S329R (AGC→CGC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,527,530 | G→T | 8.9% | intergenic (+378/‑360) | yncH → / → rhsE | DUF5445 domain‑containing protein YncH/RhsE protein in rhs element |
| RA | 1,642,447 | G→T | 13.7% | intergenic (+236/+42) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,678,082 | G→A | 7.3% | intergenic (‑179/‑345) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase subunit alpha/DUF1471 domain‑containing protein YdgH |
| RA | 1,756,214 | A→T | 6.8% | K173* (AAA→TAA) | pykF → | pyruvate kinase I |
| RA | 1,934,084 | A→C | 20.4% | V174G (GTG→GGG) | edd ← | phosphogluconate dehydratase |
| RA | 1,969,812 | A→C | 13.1% | G391G (GGT→GGG) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,045,441 | G→A | 8.3% | W168* (TGG→TGA) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,165,662 | A→T | 6.8% | intergenic (+141/‑6) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 56.7% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 55.0% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,189,102 | G→T | 17.5% | F603L (TTC→TTA) | yehB ← | putative fimbrial usher protein YehB |
| RA | 2,203,772 | Δ1 bp | 5.3% | coding (3494/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,773 | Δ1 bp | 5.3% | coding (3495/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,774 | Δ1 bp | 5.3% | coding (3496/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,775 | Δ1 bp | 5.1% | coding (3497/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,776 | Δ1 bp | 5.1% | coding (3498/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,777 | Δ1 bp | 5.1% | coding (3499/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,778 | Δ1 bp | 5.1% | coding (3500/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,203,779 | Δ1 bp | 5.1% | coding (3501/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,204,829 | T→G | 26.5% | G78G (GGT→GGG) | yehL → | putative AAA(+) MoxR family ATPase YehL |
| RA | 2,255,040 | Δ1 bp | 7.0% | coding (147/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,041 | Δ1 bp | 7.3% | coding (146/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,042 | Δ1 bp | 7.3% | coding (145/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,043 | Δ1 bp | 7.3% | coding (144/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,044 | Δ1 bp | 7.3% | coding (143/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,045 | Δ1 bp | 7.3% | coding (142/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,046 | Δ1 bp | 7.3% | coding (141/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,047 | Δ1 bp | 7.3% | coding (140/942 nt) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| RA | 2,255,223 | C→A | 25.8% | intergenic (‑37/‑132) | rihB ← / → yeiL | pyrimidine‑specific ribonucleoside hydrolase RihB/putative DNA‑binding transcriptional regulator YeiL |
| RA | 2,308,209 | A→T | 8.7% | I136N (ATC→AAC) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,327,884 | A→C | 10.9% | V87G (GTC→GGC) | yfaP ← | DUF2135 domain‑containing protein YfaP |
| RA | 2,449,194 | A→C | 46.4% | intergenic (+37/+34) | smrB → / ← yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| RA | 2,456,853 | C→A | 21.1% | intergenic (‑41/+162) | sixA ← / ← fadJ | phosphohistidine phosphatase/3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,494,881 | A→T | 6.7% | M62L (ATG→TTG) | ypdI → | colanic acid synthesis putative lipoprotein YpdI |
| RA | 2,573,150 | C→T | 9.7% | C119Y (TGT→TAT) | eutD ← | phosphate acetyltransferase EutD |
| RA | 2,647,305 | T→G | 25.5% | K7N (AAA→AAC) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,648,707 | C→T | 5.4% | G1194D (GGC→GAC) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,763,724 | T→G | 17.0% | E477A (GAG→GCG) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,791,420 | A→C | 16.3% | T50P (ACC→CCC) | gabD → | NADP(+)‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,828,605 | A→T | 6.1% | intergenic (+89/‑16) | srlD → / → gutM | sorbitol‑6‑phosphate 2‑dehydrogenase/DNA‑binding transcriptional activator GutM |
| RA | 2,857,965 | G→A | 5.3% | L291L (CTG→CTA) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,882,559 | G→A | 8.0% | R27C (CGT→TGT) | casB ← | type I‑E CRISPR system Cascade subunit CasB |
| RA | 2,901,510 | C→T | 5.9% | L307L (CTG→TTG) | yqcE → | putative transport protein YqcE |
| RA | 3,141,468 | G→A | 5.7% | P508S (CCG→TCG) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,151,290 | G→T | 7.8% | A232E (GCG→GAG) | exbB ← | Ton complex subunit ExbB |
| RA | 3,209,163 | G→T | 9.2% | M380I (ATG→ATT) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,218,532 | A→G | 6.9% | F182S (TTT→TCT) | aer ← | aerotaxis sensor receptor, flavoprotein |
| MC JC | 3,384,721 | Δ435 bp | 100% | coding (19‑453/471 nt) | argR → | DNA‑binding transcriptional dual regulator ArgR |
| RA | 3,454,069 | G→T | 27.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,493,480 | T→C | 6.4% | F305L (TTC→CTC) | tsgA → | putative transporter TsgA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,572,554 | C→T | 9.6% | D317N (GAC→AAC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,673,132 | A→G | 5.3% | Q240R (CAG→CGG) | yhjC → | putative DNA‑binding transcriptional regulator YhjC |
| JC | 3,815,859 | Δ82 bp | 11.2% | [rph] | [rph] | |
| RA | 3,859,357 | C→T | 7.4% | V254M (GTG→ATG) | yidK ← | putative transporter YidK |
| RA | 4,099,097 | T→A | 9.3% | L151Q (CTG→CAG) | rhaR → | DNA‑binding transcriptional activator RhaR |
| RA | 4,182,820 | C→T | 52.9% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,182,917 | T→G | 16.2% | V558G (GTA→GGA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,184,578 | A→C | 24.9% | I1112L (ATC→CTC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,187,331 | T→G | 14.6% | V661G (GTT→GGT) | rpoC → | RNA polymerase subunit beta' |
| JC | 4,188,518 | Δ9 bp | 6.3% | coding (3169‑3177/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,225,553 | C→T | 7.0% | R576C (CGC→TGC) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,260,234 | T→A | 5.5% | intergenic (‑231/‑87) | zur ← / → yjbL | DNA‑binding transcriptional repressor Zur/uncharacterized protein YjbL |
| RA | 4,296,060 | C→T | 29.4% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,321,301 | G→A | 6.8% | A132A (GCC→GCT) | phnG ← | carbon‑phosphorus lyase core complex subunit PhnG |
| RA | 4,547,676 | C→T | 6.5% | L861L (CTG→TTG) | fimD → | type I fimbriae usher protein |
| RA | 4,559,418 | C→T | 5.3% | A37T (GCC→ACC) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423773–3424233 | 3424524–3424239 | 7–752 | 15 [12] | [10] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 898205 | 50 (0.960) | 4 (0.080) | 4/228 | NT | 5.8% | coding (217/489 nt) | ybjO | putative inner membrane protein |
| ? | NC_000913 | 2884187 = | 82 (1.610) | intergenic (‑49/+366) | casA/cas3 | type I‑E CRISPR system Cascade subunit CasA/CRISPR‑associated endonuclease/helicase Cas3 | |||||
| * | ? | NC_000913 | 1207790 = | 21 (0.400) | 24 (0.530) | 18/202 | NT | 57.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 17 (0.380) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 21 (0.400) | 16 (0.350) | 13/202 | NT | 47.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 17 (0.380) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 57 (1.130) | 40/226 | NT | 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 | = 2707782 | 37 (0.710) | 4 (0.080) | 4/230 | NT | 8.9% | coding (20/480 nt) | rseC | protein RseC |
| ? | NC_000913 | 4008694 = | 46 (0.900) | coding (366/621 nt) | rhtB | L‑homoserine/L‑homoserine lactone/L‑threonine exporter | |||||
| * | ? | NC_000913 | 3186097 = | NA (NA) | 4 (0.080) | 4/232 | NT | NA | noncoding (2/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3187428 | NA (NA) | intergenic (+13/‑4) | insD‑5/yqiG | IS2 insertion element protein InsB/putative outer membrane usher protein YqiG | |||||