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 | 127,613 | C→G | 21.4% | intergenic (+26/‑299) | aceF → / → lpd | pyruvate dehydrogenase, E2 subunit/lipoamide dehydrogenase |
| RA | 193,868 | G→A | 7.2% | A116A (GCG→GCA) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| RA | 198,940 | G→T | 5.2% | R338L (CGT→CTT) | bamA → | outer membrane protein assembly factor BamA |
| RA | 238,523 | G→T | 22.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 22.3% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 27.9% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,019 | C→T | 7.4% | V236V (GTG→GTA) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 320,669 | T→C | 6.8% | I148T (ATC→ACC) | rclR → | DNA‑binding transcriptional activator RclR |
| RA | 342,833 | A→G | 6.1% | intergenic (+326/‑51) | yahJ → / → yahK | putative deaminase with metallo‑dependent hydrolase domain/aldehyde reductase, NADPH‑dependent |
| RA | 445,185 | G→A | 12.1% | intergenic (+11/+117) | yajQ → / ← yajR | nucleotide binding protein/putative major facilitator superfamily transport protein YajR |
| RA | 508,762 | C→T | 8.9% | intergenic (+203/+113) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator YbaQ/Cu(+) exporting P‑type ATPase |
| RA | 747,413 | A→G | 9.7% | P119P (CCT→CCC) | abrB ← | putative regulator |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,016,666 | C→T | 8.4% | W545* (TGG→TAG) | ycbZ ← | putative ATP‑dependent protease YcbZ |
| RA | 1,055,426 | T→A | 8.3% | E251D (GAA→GAT) | torS ← | sensory histidine kinase TorS |
| RA | 1,144,658 | G→C | 42.5% | V53L (GTG→CTG) | yceQ → | DUF2655 domain‑containing protein YceQ |
| RA | 1,156,651 | G→A | 7.8% | R297H (CGT→CAT) | holB → | DNA polymerase III subunit delta' |
| JC JC | 1,293,033 | IS1 (–) +14 bp | 35.8% | intergenic (‑111/‑481) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,305,018 | G→T | 8.0% | E89* (GAA→TAA) | oppD → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppD |
| RA | 1,320,747 | A→T | 14.6% | L213H (CTT→CAT) | trpD ← | anthranilate synthase subunit TrpD |
| RA | 1,626,122 | G→T | 26.9% | S420* (TCA→TAA) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,631,531 | G→T | 7.1% | T252K (ACA→AAA) | ydfJ ← | putative transporter YdfJ |
| RA | 1,671,329 | C→T | 5.6% | intergenic (+377/‑47) | ynfM → / → asr | putative transporter YnfM/acid shock protein |
| RA | 1,689,694 | A→G | 7.1% | E373E (GAA→GAG) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,840,279 | A→T | 7.7% | G271G (GGA→GGT) | ynjE → | molybdopterin synthase sulfurtransferase |
| JC JC | 1,961,829 | IS5 (–) +4 bp | 32.5% | intergenic (+34/‑140) | argS → / → yecT | arginine‑‑tRNA ligase/protein YecT |
| RA | 1,965,331 | T→C | 14.3% | K287K (AAA→AAG) | flhB ← | flagellar biosynthesis protein FlhB |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,994,454 | T→A | 8.6% | I85F (ATC→TTC) | uvrC ← | excision nuclease subunit C |
| 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 | 43.4% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 47.5% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,499,841 | G→A | 10.0% | A391T (GCT→ACT) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,503,996 | C→G | 8.9% | E164Q (GAG→CAG) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,509,690 | A→G | 6.6% | I21V (ATT→GTT) | yfeO → | putative transport protein YfeO |
| RA | 2,620,438 | C→G | 9.1% | L145L (CTG→CTC) | upp ← | uracil phosphoribosyltransferase |
| RA | 2,654,160 | G→T | 25.3% | I258I (ATC→ATA) | sseB ← | protein SseB |
| RA | 2,789,003 | G→A | 8.3% | V7I (GTA→ATA) | csiD → | PF08943 family protein CsiD |
| RA | 2,816,430 | C→A | 8.0% | D4Y (GAC→TAC) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,851,205 | G→A | 11.7% | A69T (GCA→ACA) | hypB → | hydrogenase isoenzymes nickel incorporation protein HypB |
| RA | 2,940,516 | G→T | 8.7% | P243Q (CCG→CAG) | rlmM ← | 23S rRNA 2'‑O‑ribose C2498 methyltransferase |
| RA | 2,977,328 | T→C | 9.2% | Y244H (TAT→CAT) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 3,092,229 | A→C | 21.6% | S118R (AGC→CGC) | gshB → | glutathione synthetase |
| RA | 3,184,150 | G→C | 6.2% | T106S (ACT→AGT) | ribB ← | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,190,008 | A→G | 7.2% | E43G (GAA→GGA) | yqiH → | putative fimbrial chaperone YqiH |
| RA | 3,288,038 | G→T | 33.4% | intergenic (+28/‑52) | yraH → / → yraI | putative fimbrial protein YraH/putative fimbrial chaperone YraI |
| RA | 3,486,145 | A→C | 16.1% | D9A (GAC→GCC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,497,596 | T→C | 5.9% | S198S (TCT→TCC) | nirC → | nitrite transporter NirC |
| RA | 3,534,814 | C→A | 9.7% | G352V (GGC→GTC) | envZ ← | sensory histidine kinase EnvZ |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,609,406 | G→T | 15.4% | G64C (GGC→TGC) | yhhQ → | putative queuosine precursor transporter |
| RA | 3,682,143 | C→T | 6.8% | intergenic (‑203/+18) | yhjJ ← / ← dctA | peptidase M16 family protein/C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,687,224 | G→A | 9.0% | A650A (GCC→GCT) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | 3,828,980 | A→C | 49.9% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,846,071 | C→T | 8.5% | G366D (GGC→GAC) | uhpT ← | hexose‑6‑phosphate:phosphate antiporter |
| RA | 3,875,310 | C→T | 8.9% | intergenic (‑150/‑128) | dgoR ← / → yidX | putative DNA‑binding transcriptional regulator DgoR/putative lipoprotein YidX |
| RA | 3,986,796 | C→T | 6.8% | D363N (GAT→AAT) | hemY ← | protein HemY |
| RA | 4,142,678 | C→A | 8.2% | A50D (GCC→GAC) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,142,706 | T→A | 7.7% | D59E (GAT→GAA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,185,540 | C→A | 100% | P64Q (CCG→CAG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,188,005 | G→A | 25.9% | V886I (GTA→ATA) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,283,228 | T→G | 54.4% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,288,968 | T→C | 7.9% | L402P (CTC→CCC) | nrfA → | cytochrome c552 nitrite reductase |
| RA | 4,296,060 | C→T | 23.4% | 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 | 4,297,129 | G→T | 12.4% | intergenic (‑4/+90) | yjcO ← / ← fdhF | Sel1 repeat‑containing protein YjcO/formate dehydrogenase H |
| RA | 4,327,352 | C→T | 6.2% | A73V (GCA→GTA) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,415,939 | A→T | 6.3% | intergenic (+39/+78) | aidB → / ← yjfN | putative acyl‑CoA dehydrogenase AidB/protease activator |
| RA | 4,606,337 | A→C | 26.7% | noncoding (65/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2449144 | 2449233 | 90 | 11 [10] | [10] 11 | [smrB]–[yfcO] | [smrB],[yfcO] |
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424545–3424239 | 6–777 | 13 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 258675 | NA (NA) | 20 (0.460) | 18/236 | NT | 42.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1293038 = | 27 (0.620) | intergenic (‑116/‑489) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.560) | 20 (0.520) | 17/206 | NT | 47.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 22 (0.570) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.560) | 15 (0.390) | 13/206 | NT | 40.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 22 (0.570) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4498180 = | NA (NA) | 4 (0.090) | 4/238 | NT | NA | intergenic (+240/‑92) | intB/insC‑6 | KpLE2 phage‑like element; putative integrase/KpLE2 phage‑like element; IS2 insertion element repressor InsA |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||