mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 77,026 | G→T | 8.3% | Q92K (CAA→AAA) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 99,942 | T→C | 6.7% | L100P (CTC→CCC) | murG → | N‑acetylglucosaminyl transferase |
| RA | 155,353 | T→A | 7.0% | N25I (AAT→ATT) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 238,507 | G→T | 24.8% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 20.8% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 261,028 | T→C | 6.3% | M214T (ATG→ACG) | proB → | glutamate 5‑kinase |
| RA | 289,801 | T→A | 6.2% | M169L (ATG→TTG) | argF ← | CP4‑6 prophage; ornithine carbamoyltransferase ArgF |
| RA | 317,395 | C→T | 5.2% | intergenic (‑259/+331) | ykgA ← / ← rclC | putative DNA‑binding transcriptional regulator YkgA/reactive chlorine species resistance protein C |
| RA | 332,779 | C→T | 7.2% | L137L (CTG→TTG) | pdeL → | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| RA | 383,974 | C→T | 5.7% | A5A (GCC→GCT) | ykiC → | protein YkiC |
| RA | 401,997 | G→A | 6.4% | R84H (CGT→CAT) | phoA → | alkaline phosphatase |
| RA | 431,130 | C→T | 5.5% | *295* (TGA→TAA) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 454,877 | A→T | 48.0% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,926 | G→T | 56.7% | intergenic (+137/‑207) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 540,192 | C→T | 10.5% | A349V (GCG→GTG) | allB → | allantoinase |
| RA | 546,711 | T→C | 11.7% | F11S (TTT→TCT) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 624,823 | T→A | 32.8% | intergenic (‑313/‑62) | fepB ← / → entC | ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC |
| JC | 626,246 | Δ13 bp | 10.5% | coding (177‑189/1611 nt) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 729,372 | A→C | 29.5% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 770,688 | T→A | 6.5% | intergenic (+77/‑770) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 820,638 | C→A | 23.3% | intergenic (+50/‑155) | ybhL → / → ybhM | Bax1‑I family protein YbhL/Bax1‑I family protein YbhM |
| RA | 832,612 | C→T | 9.8% | A113A (GCG→GCA) | ybiA ← | N‑glycosidase YbiA |
| RA | 874,506 | T→C | 6.0% | F510L (TTC→CTC) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 1,236,414 | T→A | 8.9% | K276N (AAA→AAT) | ycgB ← | PF04293 family protein YcgB |
| RA | 1,331,499 | T→G | 100% | F151C (TTT→TGT) | topA → | DNA topoisomerase 1 |
| RA | 1,455,991 | C→A | 6.1% | P23T (CCG→ACG) | paaD → | phenylacetate degradation protein |
| RA | 1,541,352 | G→A | 6.2% | T413T (ACC→ACT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,635,353 | G→A | 13.0% | S165S (AGC→AGT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,674,697 | T→C | 8.0% | L262S (TTG→TCG) | tqsA → | autoinducer 2 exporter |
| RA | 1,835,725 | G→A | 8.7% | A71T (GCG→ACG) | ynjA → | AhpD‑like domain‑containing protein YnjA |
| RA | 1,880,477 | G→T | 16.6% | L95I (CTT→ATT) | leuE ← | leucine exporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,003,938 | A→C | 11.7% | T23P (ACC→CCC) | fliD → | flagellar filament capping protein |
| RA | 2,068,399 | G→C | 28.0% | intergenic (‑1078/‑236) | insH‑6 ← / → yoeA | CP4‑44 prophage; IS5 transposase and trans‑activator/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,139,598 | T→G | 33.3% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| 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 | 35.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 64.0% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,224,321 | C→T | 8.1% | A184T (GCC→ACC) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,460,962 | A→G | 7.1% | intergenic (‑28/‑344) | yfcZ ← / → fadL | DUF406 domain‑containing protein YfcZ/long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor |
| RA | 2,470,427 | C→A | 46.8% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,753,254 | T→C | 7.8% | M487T (ATG→ACG) | recN → | DNA repair protein RecN |
| RA | 2,850,165 | G→A | 6.0% | R91W (CGG→TGG) | hycA ← | regulator of the transcriptional regulator FhlA |
| RA | 3,025,846 | G→T | 26.8% | E27D (GAG→GAT) | guaD → | guanine deaminase |
| RA | 3,105,696 | C→A | 7.1% | intergenic (+184/‑18) | mltC → / → nupG | membrane‑bound lytic murein transglycosylase C/nucleoside:H(+) symporter NupG |
| RA | 3,311,892 | C→T | 6.9% | E296K (GAA→AAA) | truB ← | tRNA pseudouridine(55) synthase |
| RA | 3,418,500 | T→A | 25.3% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,454,069 | G→T | 30.2% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,483,551 | A→C | 13.2% | N117T (AAC→ACC) | yheT → | putative hydrolase YheT |
| RA | 3,486,145 | A→C | 20.2% | D9A (GAC→GCC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,580,931 | G→T | 36.4% | noncoding (86/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,580,935 | G→T | 21.8% | noncoding (82/90 nt) | ryhB ← | small regulatory RNA RyhB |
| JC | 3,581,029 | +TCATTC | 29.5% | intergenic (‑13/‑109) | ryhB ← / → yhhY | small regulatory RNA RyhB/N‑acetyltransferase YhhY |
| RA | 3,735,592 | T→C | 10.2% | L205P (CTA→CCA) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| RA | 3,821,008 | C→A | 7.9% | E55* (GAG→TAG) | ligB ← | DNA ligase B |
| RA | 3,835,646 | A→G | 6.1% | V95A (GTA→GCA) | yicJ ← | putative xyloside transporter YicJ |
| RA | 3,854,849 | T→A | 7.3% | F310I (TTT→ATT) | emrD → | multidrug efflux pump EmrD |
| RA | 4,027,738 | C→A | 7.9% | L345L (CTG→CTT) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,162,523 | A→G | 5.8% | Y250H (TAC→CAC) | trmA ← | tRNA m(5)U54 methyltransferase |
| RA | 4,182,820 | C→T | 46.6% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,187,213 | G→C | 31.1% | D622H (GAC→CAC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,188,306 | A→T | 7.2% | D986V (GAC→GTC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,283,228 | T→G | 39.4% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 31.9% | 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 | 4,343,758 | Δ1 bp | 6.1% | coding (390/1422 nt) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,378,203 | G→A | 7.1% | R248C (CGC→TGC) | ampC ← | beta‑lactamase |
| RA | 4,398,407 | G→C | 28.4% | Q332H (CAG→CAC) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,482,671 | C→T | 8.3% | L389L (CTG→CTA) | valS ← | valine‑‑tRNA ligase |
| RA | 4,510,068 | C→T | 6.3% | pseudogene (265/330 nt) | yjhV → | KpLE2 phage‑like element; putative uncharacterized protein YjhV |
| RA | 4,547,281 | C→A | 9.1% | A729E (GCA→GAA) | fimD → | type I fimbriae usher protein |
| RA | 4,625,993 | T→C | 7.4% | C28R (TGT→CGT) | radA → | DNA recombination protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 164541 | 164616 | 76 | 16 [15] | [3] 16 | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | * | ÷ | NC_000913 | 3423775–3424234 | 3424527–3424238 | 5–753 | 16 [14] | [14] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381258 = | NA (NA) | 10 (0.190) | 9/232 | NT | NA | pseudogene (3/417 nt) | yaiX | putative acyltransferase, N‑terminal fragment |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 20 (0.370) | 26 (0.560) | 17/202 | NT | 52.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.620) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 19 (0.350) | 15 (0.320) | 11/202 | NT | 39.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 29 (0.620) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 59 (1.130) | 37/226 | 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 | = 4542690 | 59 (1.090) | 4 (0.080) | 4/216 | NT | 6.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 65 (1.300) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||