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 | 18,126 | T→G | 25.9% | V213G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 126,534 | T→C | 14.3% | V280V (GTT→GTC) | aceF → | pyruvate dehydrogenase, E2 subunit |
| RA | 238,497 | G→T | 20.4% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 21.0% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 24.9% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 454,877 | A→T | 47.2% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 457,102 | Δ1 bp | 7.1% | coding (426/624 nt) | clpP → | ATP‑dependent Clp protease proteolytic subunit |
| RA | 490,041 | G→T | 6.0% | intergenic (+143/+69) | mscK → / ← ybaM | potassium dependent, small conductance mechanosensitive channel/DUF2496 domain‑containing protein YbaM |
| RA | 548,258 | A→C | 13.6% | S527R (AGC→CGC) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 729,383 | T→G | 36.9% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 867,668 | A→T | 5.8% | E50V (GAA→GTA) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 932,935 | A→T | 5.9% | D114V (GAC→GTC) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 981,973 | T→A | 9.8% | P309P (CCT→CCA) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 1,085,432 | G→T | 7.8% | S147S (TCG→TCT) | phoH → | ATP‑binding protein PhoH |
| RA | 1,157,619 | G→A | 71.3% | intergenic (+45/‑250) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,250,078 | A→G | 9.5% | F254S (TTC→TCC) | dhaK ← | dihydroxyacetone kinase subunit K |
| RA | 1,253,997 | T→G | 18.9% | K652N (AAA→AAC) | ycgV ← | putative autotransporter adhesin YcgV |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,345,141 | A→T | 8.7% | S534R (AGT→AGA) | pdeR ← | cyclic di‑GMP phosphodiesterase PdeR |
| RA | 1,377,819 | T→C | 7.5% | Y330H (TAC→CAC) | ycjS → | putative oxidoreductase YcjS |
| RA | 1,428,986 | T→C | 5.9% | intergenic (+2/‑63) | lomR → / → stfR | Rac prophage; protein LomR_1/Rac prophage; putative membrane protein |
| RA | 1,466,144 | G→T | 8.0% | pseudogene (753/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,681,750 | G→C | 24.3% | A94G (GCG→GGG) | ydgC ← | GlpM family protein |
| RA | 1,728,226 | T→A | 16.0% | G130G (GGT→GGA) | gloA → | glyoxalase I |
| RA | 1,860,130 | G→C | 27.8% | L34V (CTT→GTT) | ydjK ← | putative transporter YdjK |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,026,941 | G→A | 11.8% | S359S (AGC→AGT) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,139,598 | T→G | 35.5% | 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 | 46.1% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 62.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,272 | T→A | 21.2% | intergenic (‑68/+240) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,276 | G→C | 26.4% | intergenic (‑72/+236) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,287,982 | A→T | 7.5% | pseudogene (933/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,304,524 | C→T | 10.0% | intergenic (+131/+584) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,470,431 | G→T | 43.9% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,439 | G→C | 43.4% | D437H (GAC→CAC) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,527,737 | C→A | 7.7% | I264I (ATC→ATA) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,552,285 | A→G | 8.7% | intergenic (‑147/‑67) | ypeA ← / → amiA | putative acetyltransferase YpeA/N‑acetylmuramoyl‑L‑alanine amidase A |
| RA | 2,564,532 | G→A | 6.3% | E4K (GAA→AAA) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,622,164 | A→T | 8.3% | N323I (AAC→ATC) | purM → | phosphoribosylformylglycinamide cyclo‑ligase |
| RA | 2,708,866 | T→C | 6.8% | Y180C (TAC→TGC) | rseA ← | anti‑sigma factor |
| RA | 2,791,022 | G→A | 6.0% | A347A (GCG→GCA) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,934,731 | C→T | 6.7% | A166V (GCA→GTA) | fucP → | L‑fucose:H(+) symporter |
| RA | 2,947,021 | G→A | 7.0% | P53L (CCG→CTG) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 3,012,705 | G→A | 8.6% | A512V (GCC→GTC) | yqeB ← | XdhC‑CoxI family protein YqeB |
| RA | 3,145,497 | G→A | 8.1% | G255G (GGC→GGT) | hybO ← | hydrogenase 2 small subunit |
| RA | 3,213,792 | T→A | 6.3% | I249N (ATC→AAC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,303,066 | G→A | 7.4% | C193Y (TGT→TAT) | yhbV → | putative peptidase YhbV |
| RA | 3,332,452 | T→A | 7.7% | Y95F (TAC→TTC) | yhbE ← | inner membrane protein YhbE |
| RA | 3,377,577 | T→G | 88.5% | intergenic (‑157/+238) | sspA ← / ← rpsI | stringent starvation protein A/30S ribosomal subunit protein S9 |
| RA | 3,408,322 | T→C | 6.7% | M239T (ATG→ACG) | panF → | pantothenate:Na(+) symporter |
| RA | 3,448,257 | G→T | 41.2% | intergenic (‑108/+57) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,454,875 | G→A | 8.7% | P175L (CCC→CTC) | 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 | 3,588,461 | Δ1 bp | 8.9% | coding (720/1071 nt) | ugpC ← | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| RA | 3,605,037 | A→G | 7.4% | N20S (AAC→AGC) | yhhL → | DUF1145 domain‑containing protein YhhL |
| RA | 3,733,332 | G→A | 9.3% | D378N (GAC→AAC) | xylG → | xylose ABC transporter ATP binding subunit |
| JC | 3,815,859 | Δ82 bp | 15.5% | [rph] | [rph] | |
| RA | 3,840,696 | A→G | 10.5% | V348V (GTT→GTC) | nepI ← | purine ribonucleoside exporter |
| RA | 3,891,748 | C→T | 8.0% | S45F (TCC→TTC) | mdtL → | efflux pump MdtL |
| RA | 4,118,176 | G→A | 6.4% | intergenic (‑86/‑339) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| JC JC | 4,118,284 | IS5 (–) +4 bp | 20.5% | intergenic (‑194/‑228) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| RA | 4,200,195 | Δ1 bp | 22.9% | intergenic (+101/‑86) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,200,338 | C→T | 7.9% | Q20* (CAG→TAG) | hupA → | DNA‑binding protein HU‑alpha |
| RA | 4,207,772 | A→T | 9.5% | intergenic (‑240/‑375) | purH ← / → rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| RA | 4,283,228 | T→G | 46.7% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 16.5% | 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 | 4,392,554 | G→T | 23.0% | intergenic (+7/‑29) | glyX → / → glyY | tRNA‑Gly/tRNA‑Gly |
| RA | 4,575,598 | C→A | 8.3% | pseudogene (1464/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424524–3424238 | 5–756 | 13 [11] | [10] 12 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486122 | 3486774 | 653 | 12 [10] | [11] 12 | [crp] | [crp] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381258 = | NA (NA) | 7 (0.160) | 6/232 | 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 | 381259 = | NA (NA) | 3 (0.070) +A |
3/232 | NT | NA | pseudogene (2/417 nt) | yaiX | putative acyltransferase, N‑terminal fragment |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.620) | 32 (0.850) | 27/202 | NT | 65.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.290) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.570) | 13 (0.340) | 11/202 | NT | 44.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.290) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3588461 = | 40 (0.920) | 4 (0.100) | 4/220 | NT | 12.8% | coding (720/1071 nt) | ugpC | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| ? | NC_000913 | = 3588745 | 17 (0.410) | coding (436/1071 nt) | ugpC | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit | |||||
| * | ? | NC_000913 | 4498180 = | NA (NA) | 7 (0.160) | 7/234 | 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 | |||||