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 | 115,642 | C→T | 5.5% | R28H (CGT→CAT) | hofC ← | inner membrane protein HofC |
| RA | 171,522 | A→G | 5.5% | T21A (ACG→GCG) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| RA | 238,497 | G→T | 17.2% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 18.4% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 16.9% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 22.0% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 19.7% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 32.1% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| RA | 257,368 | G→A | 5.7% | R281H (CGT→CAT) | frsA → | fermentation‑respiration switch protein |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 350,471 | A→C | 17.1% | S154R (AGC→CGC) | prpC → | 2‑methylcitrate synthase |
| RA | 357,443 | T→A | 18.4% | Y425N (TAC→AAC) | codA → | cytosine/isoguanine deaminase |
| RA | 386,899 | G→C | 7.4% | K231N (AAG→AAC) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 497,585 | C→A | 25.2% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | 534,782 | A→G | 6.6% | V289V (GTA→GTG) | gcl → | glyoxylate carboligase |
| RA | 564,273 | T→C | 5.1% | R70G (AGG→GGG) | fimZ ← | putative LuxR family transcriptional regulator FimZ |
| RA | 613,634 | T→C | 5.1% | C300R (TGT→CGT) | fes → | enterochelin esterase |
| RA | 729,372 | A→C | 29.3% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 729,383 | T→G | 33.9% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 885,071 | G→A | 6.7% | P54S (CCG→TCG) | ybjH ← | uncharacterized protein YbjH |
| RA | 887,087 | A→G | 7.3% | S85P (TCC→CCC) | ybjJ ← | inner membrane protein YbjJ |
| RA | 905,517 | T→A | 7.5% | F202Y (TTT→TAT) | amiD → | N‑acetylmuramoyl‑L‑alanine amidase D |
| RA | 1,011,739 | G→A | 5.6% | A592A (GCG→GCA) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,295,520 | C→A | 21.0% | V868L (GTA→TTA) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,379,812 | T→C | 5.9% | D643D (GAT→GAC) | ycjT → | kojibiose phosphorylase |
| RA | 1,383,065 | C→T | 5.2% | T299T (ACG→ACA) | ycjW ← | putative LacI‑type DNA‑binding transcriptional regulator YcjW |
| RA | 1,506,088 | T→A | 6.7% | intergenic (‑8/‑84) | ydcO ← / → sutR | putative transport protein YdcO/DNA‑binding transcriptional dual regulator SutR |
| RA | 1,708,916 | A→C | 17.8% | K666N (AAA→AAC) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,834,139 | A→T | 6.4% | S8S (TCA→TCT) | ydjY → | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,077,025 | T→G | 13.1% | V70G (GTC→GGC) | yeeT → | CP4‑44 prophage; DUF987 domain‑containing protein YeeT |
| RA | 2,139,574 | A→C | 26.7% | intergenic (+89/+185) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,139,598 | T→G | 26.4% | 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 | 53.7% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 59.2% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,365,658 | A→T | 7.2% | intergenic (‑38/‑252) | ais ← / → arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| RA | 2,403,173 | C→T | 7.4% | G225R (GGG→AGG) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,449,194 | A→C | 51.9% | intergenic (+37/+34) | smrB → / ← yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| RA | 2,470,436 | C→A | 33.7% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 42.5% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,612,012 | T→C | 5.8% | L38S (TTA→TCA) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,671,328 | C→T | 6.8% | T35M (ACG→ATG) | hcaB → | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| RA | 2,725,812 | G→T | 27.5% | intergenic (‑66/+257) | kgtP ← / ← rrfG | alpha‑ketoglutarate:H(+) symporter/5S ribosomal RNA |
| RA | 2,848,548 | A→C | 13.6% | L232V (TTG→GTG) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 2,854,853 | T→A | 8.7% | V172V (GTT→GTA) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | 2,955,107 | C→T | 8.3% | K299K (AAG→AAA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,965,841 | A→T | 5.5% | L66H (CTC→CAC) | lgt ← | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase |
| RA | 3,269,418 | T→A | 15.7% | L335* (TTA→TAA) | yhaC → | uncharacterized protein YhaC |
| MC JC | 3,384,721 | Δ435 bp | 100% | coding (19‑453/471 nt) | argR → | DNA‑binding transcriptional dual regulator ArgR |
| RA | 3,393,072 | T→A | 5.1% | I1063F (ATT→TTT) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,418,500 | T→A | 27.4% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,454,087 | C→A | 16.0% | E438* (GAA→TAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,541,236 | T→A | 5.5% | I277N (ATC→AAC) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,775,361 | G→T | 6.1% | G313V (GGT→GTT) | mtlD → | mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,801,330 | T→C | 5.6% | K224E (AAA→GAA) | waaJ ← | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| RA | 3,815,815 | T→G | 11.1% | intergenic (‑47/+48) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| RA | 3,815,824 | G→T | 60.8% | intergenic (‑56/+39) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| JC | 3,815,859 | Δ82 bp | 11.4% | [rph] | [rph] | |
| RA | 3,847,461 | A→G | 11.4% | F388F (TTT→TTC) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| RA | 3,868,779 | A→G | 5.0% | F177F (TTT→TTC) | yidR ← | DUF3748 domain‑containing galacturonate catabolism protein YidR |
| RA | 3,904,917 | G→T | 7.3% | C227* (TGC→TGA) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,955,638 | T→G | 23.2% | V103G (GTG→GGG) | ilvA → | threonine deaminase |
| RA | 4,051,729 | G→A | 6.4% | W128* (TGG→TAG) | yihI → | Der GTPase‑activating protein YihI |
| JC | 4,188,495 | Δ3 bp | 16.8% | coding (3146‑3148/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,188,513 | G→T | 62.3% | G1055V (GGT→GTT) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,201,731 | T→A | 6.1% | intergenic (‑43/‑195) | zraP ← / → zraS | zinc responsive, periplasmic protein with chaperone activity/sensory histidine kinase ZraS |
| RA | 4,220,007 | T→G | 51.2% | V471G (GTG→GGG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,220,018 | G→T | 39.0% | D475Y (GAT→TAT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,237,023 | T→C | 8.3% | L43L (TTA→CTA) | yjbG → | capsule biosynthesis GfcC family protein YjbG |
| RA | 4,296,060 | C→T | 28.7% | 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 | 4,606,203 | T→G | 42.9% | noncoding (84/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,613,308 | A→C | 36.5% | T300P (ACG→CCG) | yjjU → | putative patatin‑like phospholipase YjjU |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424527–3424239 | 6–759 | 23 [16] | [17] 24 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.500) | 25 (0.450) | 19/206 | NT | 45.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 33 (0.600) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.500) | 25 (0.450) | 16/206 | NT | 45.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 33 (0.600) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 84 (1.360) | 44/230 | 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 | 69 (1.080) | 4 (0.070) | 4/220 | NT | 5.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 69 (1.170) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||