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 | 123,466 | T→G | 25.7% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 238,523 | G→T | 21.4% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 31.0% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 514,196 | Δ1 bp | 6.3% | coding (204/408 nt) | cueR → | DNA‑binding transcriptional dual regulator CueR |
| RA | 548,153 | T→G | 21.1% | L492V (TTA→GTA) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 594,741 | A→G | 7.5% | F10F (TTT→TTC) | cusS ← | sensory histidine kinase CusS |
| RA | 624,819 | A→T | 22.7% | intergenic (‑309/‑66) | fepB ← / → entC | ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC |
| RA | 628,877 | C→A | 53.0% | N109K (AAC→AAA) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| RA | 681,694 | A→C | 36.5% | intergenic (+31/+29) | djlC → / ← hscC | co‑chaperone DjlC/chaperone protein HscC |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 715,084 | A→T | 6.9% | S509S (TCA→TCT) | pgm → | phosphoglucomutase |
| RA | 729,372 | A→C | 28.4% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 767,969 | G→C | 21.0% | intergenic (+9/‑9) | mngA → / → mngB | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II/alpha‑mannosidase |
| RA | 821,750 | A→G | 6.6% | V250A (GTG→GCG) | ybhN ← | conserved inner membrane protein YbhN |
| RA | 846,714 | G→A | 7.9% | R136C (CGC→TGC) | glnP ← | L‑glutamine ABC transporter membrane subunit |
| RA | 968,690 | Δ1 bp | 7.4% | coding (325/987 nt) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 970,649 | Δ1 bp | 8.5% | intergenic (+28/‑24) | ycaQ → / → ycaR | winged helix DNA‑binding domain‑containing protein YcaQ/UPF0434 family protein YcaR |
| RA | 1,002,283 | C→T | 6.9% | S159S (AGC→AGT) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,003,034 | C→T | 7.0% | A49V (GCA→GTA) | ycbU → | putative fimbrial protein YcbU |
| RA | 1,082,145 | T→C | 6.1% | pseudogene (790/830 nt) | efeU → | inactive ferrous iron permease EfeU, N‑terminal fragment |
| RA | 1,086,101 | G→A | 5.3% | intergenic (+45/+5) | phoH → / ← pgaD | ATP‑binding protein PhoH/poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaD |
| RA | 1,133,605 | G→A | 6.1% | L344L (TTG→TTA) | flgE → | flagellar hook protein FlgE |
| RA | 1,267,580 | G→A | 7.1% | L87L (CTG→CTA) | ychA → | transglutaminase‑like/TPR repeat‑containing protein |
| RA | 1,297,596 | C→T | 9.0% | E176K (GAA→AAA) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,331,499 | T→G | 100% | F151C (TTT→TGT) | topA → | DNA topoisomerase 1 |
| RA | 1,365,875 | C→G | 5.8% | T109S (ACC→AGC) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| RA | 1,491,952 | A→G | 6.7% | V40V (GTT→GTC) | hokB ← | toxin HokB |
| RA | 1,505,719 | G→A | 9.9% | P121L (CCG→CTG) | ydcO ← | putative transport protein YdcO |
| RA | 1,512,268 | G→A | 6.4% | L205L (TTG→TTA) | ydcS → | putative ABC transporter periplasmic binding protein/polyhydroxybutyrate synthase |
| RA | 1,692,581 | C→T | 5.8% | A91T (GCT→ACT) | uidC ← | outer membrane porin family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,981,537 | C→T | 6.7% | V26I (GTT→ATT) | otsA ← | trehalose‑6‑phosphate synthase |
| 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 | 60.2% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 67.4% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,180,646 | T→A | 7.4% | I184I (ATT→ATA) | yegU → | putative ADP‑ribosylglycohydrolase YegU |
| RA | 2,358,284 | C→T | 5.6% | D188N (GAT→AAT) | yfaU ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| RA | 2,358,737 | T→C | 5.3% | T37A (ACT→GCT) | yfaU ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| RA | 2,408,908 | T→C | 5.6% | I16T (ATT→ACT) | yfbR → | dCMP phosphohydrolase |
| RA | 2,470,439 | G→C | 31.4% | D437H (GAC→CAC) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 28.4% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,661,449 | G→A | 8.9% | T28M (ACG→ATG) | iscS ← | cysteine desulfurase |
| RA | 2,703,369 | A→T | 5.3% | S6R (AGT→AGA) | era ← | 30S ribosomal subunit maturation GTPase Era |
| RA | 2,749,909 | T→C | 6.1% | V379A (GTC→GCC) | yfjD → | putative inner membrane protein |
| RA | 3,010,788 | C→A | 5.4% | A254E (GCG→GAG) | hyuA → | phenylhydantoinase |
| RA | 3,078,793 | G→A | 7.3% | P23S (CCC→TCC) | cmtA ← | mannitol‑specific PTS enzyme IICB component CmtA |
| RA | 3,283,152 | A→G | 5.8% | I4V (ATC→GTC) | kbaY → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaY |
| RA | 3,315,157 | T→C | 8.2% | K286K (AAA→AAG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,390,002 | G→A | 9.2% | M161I (ATG→ATA) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,454,062 | C→G | 18.1% | S446T (AGC→ACC) | gspA ← | Type II secretion system protein GspA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,580,931 | G→T | 84.7% | noncoding (86/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,736,878 | G→A | 6.2% | N100N (AAC→AAT) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,736,889 | C→A | 6.2% | A97S (GCG→TCG) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,828,985 | T→G | 27.1% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,933,230 | G→T | 16.3% | intergenic (+46/‑121) | kup → / → rbsD | K(+):H(+) symporter Kup/D‑ribose pyranase |
| RA | 3,998,496 | A→T | 9.1% | K172* (AAG→TAG) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 3,998,508 | G→T | 8.1% | A176S (GCG→TCG) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 4,182,820 | C→T | 100% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,248,751 | A→T | 5.8% | T261S (ACT→TCT) | lamB → | maltose outer membrane channel/phage lambda receptor protein |
| RA | 4,296,060 | C→T | 17.5% | 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 | 4,400,313 | A→G | 9.7% | D9G (GAT→GGT) | hfq → | RNA‑binding protein Hfq |
| RA | 4,417,619 | G→T | 6.0% | C223F (TGT→TTT) | yjfP → | carboxylesterase |
| RA | 4,481,887 | A→C | 22.0% | F651V (TTT→GTT) | valS ← | valine‑‑tRNA ligase |
| RA | 4,600,882 | Δ1 bp | 6.3% | coding (94/738 nt) | dnaC ← | DNA replication protein DnaC |
| RA | 4,600,883 | Δ1 bp | 6.3% | coding (93/738 nt) | dnaC ← | DNA replication protein DnaC |
| RA | 4,619,538 | G→A | 6.2% | R437H (CGT→CAT) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424551–3424239 | 6–782 | 18 [16] | [16] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 33 (0.560) | 34 (0.670) | 21/202 | NT | 58.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.380) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.580) | 20 (0.400) | 17/202 | NT | 45.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.380) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 91 (1.610) | 57/226 | 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 | 1467910 = | NA (NA) | 4 (0.070) | 4/234 | NT | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469241 | NA (NA) | intergenic (‑92/‑5) | insC‑2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 4542682 = | 48 (0.820) | 4 (0.070) | 4/216 | NT | 6.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 64 (1.180) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||