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 | 87,881 | A→G | 8.6% | intergenic (+33/‑147) | ilvH → / → cra | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra |
| RA | 87,884 | T→A | 7.9% | intergenic (+36/‑144) | ilvH → / → cra | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra |
| RA | 87,887 | C→T | 9.3% | intergenic (+39/‑141) | ilvH → / → cra | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 167,293 | G→C | 6.3% | intergenic (+29/‑191) | mrcB → / → fhuA | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor |
| RA | 167,295 | T→C | 6.1% | intergenic (+31/‑189) | mrcB → / → fhuA | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor |
| RA | 187,458 | C→T | 10.0% | R398H (CGC→CAC) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 459,834 | C→A | 100% | A316E (GCG→GAG) | lon → | Lon protease |
| RA | 464,356 | A→T | 6.2% | intergenic (+48/‑46) | ybaV → / → fadM | helix‑hairpin‑helix 3 family protein/thioesterase III |
| RA | 539,504 | G→A | 7.3% | A120T (GCG→ACG) | allB → | allantoinase |
| RA | 543,091 | G→C | 9.0% | intergenic (+58/+170) | glxK → / ← allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase |
| RA | 543,094 | G→C | 10.6% | intergenic (+61/+167) | glxK → / ← allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 897,968:1 | +A | 6.8% | intergenic (+39/‑21) | potI → / → ybjO | putrescine ABC transporter membrane subunit PotI/putative inner membrane protein |
| RA | 897,973 | Δ1 bp | 6.8% | intergenic (+44/‑16) | potI → / → ybjO | putrescine ABC transporter membrane subunit PotI/putative inner membrane protein |
| RA | 1,015,912 | T→A | 5.8% | intergenic (+30/+40) | rmf → / ← fabA | ribosome modulation factor/beta‑hydroxyacyl‑acyl carrier protein dehydratase/isomerase |
| RA | 1,169,380 | T→C | 8.6% | intergenic (+50/+32) | bhsA → / ← ldtC | DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA/L,D‑transpeptidase YcfS |
| RA | 1,169,382 | C→G | 7.3% | intergenic (+52/+30) | bhsA → / ← ldtC | DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA/L,D‑transpeptidase YcfS |
| RA | 1,169,384 | G→A | 7.4% | intergenic (+54/+28) | bhsA → / ← ldtC | DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA/L,D‑transpeptidase YcfS |
| RA | 1,196,220 | C→T | 44.1% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 41.8% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 35.7% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 35.0% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,440,791 | C→T | 32.4% | intergenic (‑7/‑267) | ydbK ← / → ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ |
| RA | 1,466,504 | A→G | 14.4% | pseudogene (1113/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,684,016 | A→G | 11.4% | S379G (AGC→GGC) | rstB → | sensory histidine kinase RstB |
| RA | 1,684,019 | C→T | 10.5% | R380W (CGG→TGG) | rstB → | sensory histidine kinase RstB |
| RA | 1,708,814 | A→G | 13.5% | A632A (GCA→GCG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,864,758 | G→A | 6.2% | intergenic (+24/+24) | yeaD → / ← yeaE | putative aldose 1‑epimerase YeaD/methylglyoxal reductase YeaE |
| RA | 1,864,763 | A→T | 6.3% | intergenic (+29/+19) | yeaD → / ← yeaE | putative aldose 1‑epimerase YeaD/methylglyoxal reductase YeaE |
| RA | 1,883,027 | C→G | 6.5% | intergenic (+30/‑161) | dmlA → / → yeaV | D‑malate/3‑isopropylmalate dehydrogenase (decarboxylating)/putative transporter YeaV |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 1,985,112 | C→G | 13.2% | intergenic (‑43/+27) | araG ← / ← araF | arabinose ABC transporter ATP binding subunit/arabinose ABC transporter periplasmic binding protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,383,956 | A→T | 8.2% | intergenic (+32/+39) | elaD → / ← yfbK | protease ElaD/IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,383,959 | A→T | 8.6% | intergenic (+35/+36) | elaD → / ← yfbK | protease ElaD/IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,430,144 | G→C | 6.9% | A32G (GCC→GGC) | purF ← | amidophosphoribosyltransferase |
| RA | 2,513,638 | A→G | 7.8% | V199V (GTA→GTG) | nupC → | nucleoside:H(+) symporter NupC |
| RA | 2,521,344 | C→T | 8.2% | intergenic (+16/+249) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,521,346 | A→T | 8.7% | intergenic (+18/+247) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,521,348 | A→G | 9.9% | intergenic (+20/+245) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,592,990 | A→C | 6.7% | intergenic (+28/+82) | ypfN → / ← ypfH | UPF0370 protein YpfN/esterase YpfH |
| RA | 2,637,438 | T→G | 7.3% | intergenic (‑82/+36) | der ← / ← bamB | 50S ribosomal subunit stability factor/outer membrane protein assembly factor BamB |
| RA | 2,637,444 | A→G | 7.5% | intergenic (‑88/+30) | der ← / ← bamB | 50S ribosomal subunit stability factor/outer membrane protein assembly factor BamB |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,679,430 | Δ1 bp | 7.8% | intergenic (‑63/+34) | yphF ← / ← yphG | putative ABC transporter periplasmic binding protein YphF/DUF5107 domain‑containing protein YphG |
| RA | 2,679,434:1 | +C | 7.8% | intergenic (‑67/+30) | yphF ← / ← yphG | putative ABC transporter periplasmic binding protein YphF/DUF5107 domain‑containing protein YphG |
| RA | 2,724,099 | T→G | 7.3% | intergenic (+17/‑29) | pssA → / → yfiM | phosphatidylserine synthase/protein YfiM |
| RA | 2,866,487 | G→C | 6.3% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter YgbN/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,866,488 | G→C | 5.4% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter YgbN/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,917,909 | T→G | 6.2% | intergenic (+96/+136) | barA → / ← gudD | sensory histidine kinase BarA/D‑glucarate dehydratase |
| RA | 2,976,320 | T→G | 6.4% | noncoding (66/82 nt) | omrB ← | small regulatory RNA OmrB |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,131,524 | A→G | 9.5% | S295S (AGT→AGC) ‡ | yghQ ← | putative transport protein YghQ |
| RA | 3,131,525 | C→T | 8.2% | S295N (AGT→AAT) ‡ | yghQ ← | putative transport protein YghQ |
| RA | 3,156,590 | C→A | 6.3% | intergenic (+72/‑33) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,156,591 | T→G | 6.1% | intergenic (+73/‑32) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,368,982 | G→C | 7.2% | intergenic (+28/+32) | yhcG → / ← yhcH | DUF1016 domain‑containing protein YhcG/DUF386 domain‑containing protein YhcH |
| RA | 3,473,615 | C→T | 100% | W156* (TGG→TAG) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,959,926 | A→T | 5.5% | intergenic (‑113/+86) | ppiC ← / ← yifN | peptidyl‑prolyl cis‑trans isomerase C/putative toxin YifN |
| JC | 4,001,645 | Δ5 bp | 94.3% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,082,474 | G→C | 6.5% | R96G (CGC→GGC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,286,116 | C→G | 7.0% | G419A (GGC→GCC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,060 | C→T | 17.7% | 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 | 4,325,285 | G→C | 6.9% | intergenic (‑120/+13) | phnC ← / ← yjdN | phosphonate ABC transporter ATP binding subunit/conserved protein YjdN |
| RA | 4,385,146 | T→C | 6.1% | I436I (ATT→ATC) | yjeM → | putative transporter YjeM |
| RA | 4,472,434 | G→A | 7.6% | R34* (CGA→TGA) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,472,437 | T→C | 11.0% | N33D (AAT→GAT) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,479,016 | G→C | 6.5% | intergenic (+127/+18) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,479,020 | A→T | 6.6% | intergenic (+131/+14) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,624,433 | T→C | 7.7% | K119K (AAA→AAG) | ytjB ← | protein Smp |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 365842 | 366435 | 594 | 24 [23] | [23] 26 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913 | 1209574 | 1209634 | 61 | 24 [23] | [23] 24 | stfE | e14 prophage; putative side tail fiber protein fragment |
| * | * | ÷ | NC_000913 | 2818104–2818129 | 2818247–2818198 | 70–144 | 24 [23] | [23] 24 | [argZ]–[argY] | [argZ],[argY] |
| * | * | ÷ | NC_000913 | 3423739–3424234 | 3424528–3424238 | 5–790 | 24 [23] | [23] 28 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 93541 | 50 (0.870) | 3 (0.050) | 3/258 | NT | 5.8% | coding (376/1488 nt) | murE | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| ? | NC_000913 | = 93563 | 48 (0.860) | coding (398/1488 nt) | murE | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase | |||||
| * | ? | NC_000913 | = 315413 | NA (NA) | 3 (0.060) | 3/238 | NT | NA | noncoding (185/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315613 | NA (NA) | noncoding (385/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315520 | NA (NA) | 3 (0.060) | 3/250 | NT | NA | noncoding (292/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315537 | NA (NA) | noncoding (309/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315646 | NA (NA) | 10 (0.180) | 7/254 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315651 | NA (NA) | 4 (0.070) | 4/248 | NT | NA | noncoding (423/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315703 | NA (NA) | noncoding (475/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315852 | NA (NA) | 32 (0.580) | 11/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 4 (0.080) | 4/246 | NT | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 501495 = | NA (NA) | 4 (0.070) | 4/256 | NT | NA | noncoding (3/36 nt) | other | REP46b |
| ? | NC_000913 | 501521 = | NA (NA) | noncoding (29/36 nt) | other | REP46b | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2490 (43.830) | 252/262 | NT | 97.7% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 58 (1.010) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 58 (1.010) | 14 (0.330) +34 bp |
9/196 | NT | 31.0% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 26 (0.450) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 774622 | 36 (0.630) | 5 (0.090) | 3/252 | NT | 14.0% | intergenic (+20/‑130) | ybgE/ybgC | cyd operon protein YbgE/esterase/thioesterase |
| ? | NC_000913 | = 774648 | 27 (0.490) | intergenic (+46/‑104) | ybgE/ybgC | cyd operon protein YbgE/esterase/thioesterase | |||||
| * | ? | NC_000913 | 1026664 = | 46 (0.800) | 3 (0.060) | 3/250 | NT | 6.8% | coding (352/459 nt) | mgsA | methylglyoxal synthase |
| ? | NC_000913 | 1026694 = | 39 (0.720) | coding (322/459 nt) | mgsA | methylglyoxal synthase | |||||
| * | ? | NC_000913 | 1207790 = | 1 (0.020) | 20 (0.400) | 18/232 | NT | 97.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.020) | 11 (0.220) | 11/232 | NT | 96.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1414530 = | 43 (0.750) | 3 (0.050) | 3/262 | NT | 5.5% | coding (264/810 nt) | recT | Rac prophage; recombinase, DNA renaturation |
| ? | NC_000913 | = 1449280 | 60 (1.060) | coding (2070/2274 nt) | tynA | copper‑containing amine oxidase | |||||
| * | ? | NC_000913 | 1421002 = | 49 (0.860) | 4 (0.070) | 4/258 | NT | 6.3% | coding (319/423 nt) | ydaT | Rac prophage; protein YdaT |
| ? | NC_000913 | = 1446373 | 71 (1.270) | intergenic (+167/+5) | ydbL/feaR | DUF1318 domain‑containing protein YdbL/DNA‑binding transcriptional activator FeaR | |||||
| * | ? | NC_000913 | 1436950 = | 48 (0.840) | 7 (0.120) | 7/262 | NT | 10.6% | intergenic (‑57/‑171) | ompN/micC | outer membrane porin N/small regulatory RNA MicC |
| ? | NC_000913 | = 1458936 | 70 (1.230) | coding (673/789 nt) | paaG | putative ring 1,2‑epoxyphenylacetyl‑CoA isomerase (oxepin‑CoA forming) | |||||
| * | ? | NC_000913 | 1437016 = | 59 (1.030) | 15 (0.260) | 14/262 | NT | 22.8% | intergenic (‑123/‑105) | ompN/micC | outer membrane porin N/small regulatory RNA MicC |
| ? | NC_000913 | = 1550731 | 43 (0.760) | coding (271/885 nt) | fdnH | formate dehydrogenase N subunit beta | |||||
| * | ? | NC_000913 | 2524489 = | 59 (1.030) | 3 (0.050) | 3/252 | NT | 5.3% | coding (390/834 nt) | xapA | xanthosine phosphorylase |
| ? | NC_000913 | 2524527 = | 50 (0.920) | coding (352/834 nt) | xapA | xanthosine phosphorylase | |||||
| * | ? | NC_000913 | 3042324 = | NA (NA) | 3 (0.050) | 3/256 | NT | NA | noncoding (3/36 nt) | other | REP210a |
| ? | NC_000913 | 3042350 = | NA (NA) | noncoding (29/36 nt) | other | REP210a | |||||
| * | ? | NC_000913 | = 4168341 | 29 (0.510) | 3 (0.060) | 3/244 | NT | 10.0% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| ? | NC_000913 | = 4168363 | 27 (0.510) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu | |||||
| * | ? | NC_000913 | 4343130 = | 49 (0.860) | 3 (0.050) | 3/252 | NT | 6.0% | coding (1220/1356 nt) | melA | alpha‑galactosidase |
| ? | NC_000913 | 4343158 = | 48 (0.880) | coding (1248/1356 nt) | melA | alpha‑galactosidase | |||||
| * | ? | NC_000913 | 4636324 = | 58 (1.010) | 4 (0.070) | 4/250 | NT | 6.7% | coding (318/690 nt) | creB | DNA‑binding transcriptional regulator CreB |
| ? | NC_000913 | 4636375 = | 56 (1.030) | coding (369/690 nt) | creB | DNA‑binding transcriptional regulator CreB | |||||