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 | 87,218 | A→G | 8.3% | E530G (GAG→GGG) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 123,466 | T→G | 32.1% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 123,475 | C→G | 31.1% | F153L (TTC→TTG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 189,075 | A→T | 7.1% | I144I (ATT→ATA) | map ← | methionine aminopeptidase |
| RA | 238,497 | G→T | 14.2% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 14.1% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 17.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 268,011 | Δ1 bp | 5.7% | intergenic (‑6/+86) | yafZ ← / ← ykfA | CP4‑6 prophage; conserved protein YafZ/CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 268,012 | Δ1 bp | 5.6% | intergenic (‑7/+85) | yafZ ← / ← ykfA | CP4‑6 prophage; conserved protein YafZ/CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 268,013 | Δ1 bp | 6.0% | intergenic (‑8/+84) | yafZ ← / ← ykfA | CP4‑6 prophage; conserved protein YafZ/CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 268,014 | Δ1 bp | 6.0% | intergenic (‑9/+83) | yafZ ← / ← ykfA | CP4‑6 prophage; conserved protein YafZ/CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 284,554 | A→T | 8.7% | K452* (AAG→TAG) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 422,429 | T→G | 28.7% | intergenic (+70/‑89) | proY → / → malZ | putative transporter ProY/maltodextrin glucosidase |
| RA | 454,877 | A→T | 36.3% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 543,341 | G→T | 6.6% | Q236K (CAG→AAG) | allE ← | (S)‑ureidoglycine aminohydrolase |
| RA | 556,637 | T→G | 29.2% | intergenic (‑84/+24) | ybcI ← / ← ybcJ | conserved inner membrane protein YbcI/putative RNA‑binding protein YbcJ |
| RA | 586,610 | A→G | 5.4% | L100P (CTA→CCA) | envY ← | DNA‑binding transcriptional activator EnvY |
| RA | 693,037 | T→G | 17.6% | K114N (AAA→AAC) | ybeZ ← | PhoH‑like protein |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 729,383 | T→G | 34.8% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| JC JC | 771,306 | IS5 (+) +4 bp | 12.6% | intergenic (+695/‑149) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| JC JC | 771,322 | IS5 (+) +4 bp | 10.0% | intergenic (+711/‑133) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 783,071 | G→A | 5.4% | E329E (GAG→GAA) | nadA → | quinolinate synthase |
| RA | 903,765 | A→C | 8.2% | intergenic (‑31/+187) | artP ← / ← ybjP | L‑arginine ABC transporter ATP binding subunit/DUF3828 domain‑containing lipoprotein YbjP |
| RA | 1,047,005 | T→A | 7.8% | K314M (AAG→ATG) | gfcD ← | putative lipoprotein GfcD |
| JC JC | 1,293,222 | IS5 (+) +4 bp | 8.2% | intergenic (‑300/‑302) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,334,411 | T→C | 7.1% | I186T (ATT→ACT) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,334,423 | C→T | 7.5% | A190V (GCG→GTG) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,434,986 | C→A | 26.2% | pseudogene (23/51 nt) | ttcC ← | putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,830,701 | G→A | 7.3% | T22M (ACG→ATG) | astA ← | arginine N‑succinyltransferase |
| RA | 1,916,844 | C→G | 11.0% | A196G (GCG→GGG) | yebS → | intermembrane transport protein YebS |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,077,677 | A→G | 7.1% | T37A (ACA→GCA) | cbtA → | CP4‑44 prophage; cytoskeleton‑binding toxin CbtA |
| RA | 2,078,318 | C→A | 16.6% | intergenic (+184/‑257) | yeeW → / → yoeF | CP4‑44 prophage; putative uncharacterized protein YeeW/CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,139,598 | T→G | 37.9% | 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 | 2,177,245 | G→T | 100% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,270 | G→T | 28.8% | intergenic (‑66/+242) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,194,544 | A→T | 7.1% | Q82L (CAG→CTG) | metG → | methionine‑‑tRNA ligase |
| RA | 2,208,054 | G→A | 7.5% | G30R (GGG→AGG) | yehP → | VWA domain‑containing protein YehP |
| RA | 2,284,842 | G→T | 7.0% | S156I (AGC→ATC) | yejM → | putative cardiolipin transport protein |
| RA | 2,314,181 | G→T | 25.7% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,449,102 | C→T | 9.7% | A166V (GCG→GTG) | smrB → | putative endonuclease SmrB |
| RA | 2,470,427 | C→A | 40.7% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 32.2% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 38.2% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,655,531 | A→T | 5.4% | T276T (ACT→ACA) | pepB ← | aminopeptidase B |
| RA | 2,780,200 | C→T | 5.4% | G843R (GGA→AGA) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,821,684 | A→G | 6.4% | F110L (TTT→CTT) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 3,100,046 | G→T | 6.0% | S228Y (TCT→TAT) | ansB ← | L‑asparaginase 2 |
| RA | 3,398,608 | G→A | 5.6% | L90L (CTG→TTG) | mreD ← | cell shape determining protein MreD |
| RA | 3,418,500 | T→A | 31.1% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,445,093 | A→C | 16.2% | V46G (GTT→GGT) | rpsE ← | 30S ribosomal subunit protein S5 |
| RA | 3,454,087 | C→A | 23.1% | E438* (GAA→TAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,464,588 | T→C | 5.4% | Y223H (TAT→CAT) | gspL → | Type II secretion system protein GspL |
| RA | 3,482,567 | G→C | 32.4% | E427Q (GAA→CAA) | yheS → | ABC transporter ATP‑binding protein YheS |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,580,933 | C→G | 81.0% | noncoding (84/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,609,240 | A→G | 6.3% | Q8Q (CAA→CAG) | yhhQ → | putative queuosine precursor transporter |
| RA | 3,828,980 | A→C | 47.4% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,833,792 | G→A | 5.7% | A249V (GCG→GTG) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 4,084,273 | G→A | 7.8% | A517V (GCG→GTG) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,182,929 | A→T | 100% | E562V (GAA→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 24.6% | 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 | 4,313,089 | T→C | 100% | intergenic (‑98/‑261) | alsR ← / → rpiB | DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B |
| RA | 4,385,998 | C→A | 8.0% | R99S (CGC→AGC) | yjeO → | conserved inner membrane protein YjeO |
| RA | 4,481,370 | T→G | 17.0% | E823A (GAG→GCG) | valS ← | valine‑‑tRNA ligase |
| RA | 4,617,646 | C→T | 9.3% | R108R (CGC→CGT) | deoC → | deoxyribose‑phosphate aldolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423776–3424234 | 3424527–3424238 | 5–752 | 15 [14] | [11] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 574591 = | NA (NA) | 4 (0.080) | 4/226 | NT | 6.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 771409 = | 56 (1.080) | intergenic (+798/‑49) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I | |||||
| * | ? | NC_000913 | = 625311 | 11 (0.210) | 32 (0.630) | 26/228 | NT | 78.3% | coding (427/1176 nt) | entC | isochorismate synthase EntC |
| ? | NC_000913 | 626255 = | 7 (0.140) | coding (186/1611 nt) | entE | 2,3‑dihydroxybenzoate‑AMP ligase | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.480) | 27 (0.600) | 21/202 | NT | 57.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.420) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.480) | 14 (0.310) | 10/202 | NT | 40.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.420) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 36 (0.690) | 4 (0.080) | 4/216 | NT | 8.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 56 (1.170) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 33 (0.630) | 10 (0.210) | 9/216 | NT | 18.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 56 (1.170) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||