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 | 7,677 | T→A | 20.7% | M95L (ATG→TTG) | yaaJ ← | putative transporter YaaJ |
| RA | 114,833 | G→A | 5.6% | Q298* (CAA→TAA) | hofC ← | inner membrane protein HofC |
| RA | 123,437 | C→T | 38.3% | Q141* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 127,642 | G→T | 21.5% | intergenic (+55/‑270) | aceF → / → lpd | pyruvate dehydrogenase, E2 subunit/lipoamide dehydrogenase |
| RA | 173,472 | T→G | 33.5% | intergenic (+28/+130) | fhuB → / ← hemL | iron(III) hydroxamate ABC transporter membrane subunit/glutamate‑1‑semialdehyde aminotransferase |
| RA | 238,497 | G→T | 14.3% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 23.0% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 19.0% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 20.8% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 28.3% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 337,205 | T→C | 7.2% | F143S (TTT→TCT) | yahF → | putative acyl‑CoA synthetase YahF |
| RA | 386,783 | G→T | 100% | V193L (GTG→TTG) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 431,860 | G→A | 7.0% | Q52* (CAG→TAG) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 454,901 | C→A | 25.7% | intergenic (+112/‑232) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 497,594 | G→C | 34.0% | P140P (CCG→CCC) | adk → | adenylate kinase |
| RA | 523,495 | A→C | 20.8% | S79R (AGC→CGC) | rhsD → | protein RhsD |
| RA | 556,637 | T→G | 27.8% | intergenic (‑84/+24) | ybcI ← / ← ybcJ | conserved inner membrane protein YbcI/putative RNA‑binding protein YbcJ |
| RA | 626,053 | T→C | 11.7% | L390S (TTG→TCG) | entC → | isochorismate synthase EntC |
| RA | 669,902 | T→C | 89.1% | R2R (CGA→CGG) | cobC ← | putative adenosylcobalamin phosphatase/alpha‑ribazole phosphatase |
| RA | 684,348 | G→A | 5.8% | A22V (GCC→GTC) | rihA ← | pyrimidine‑specific ribonucleoside hydrolase RihA |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 965,166 | C→T | 6.1% | R283C (CGT→TGT) | ycaI → | conserved inner membrane protein YcaI |
| RA | 1,063,155 | G→C | 7.6% | V207V (GTC→GTG) | cbpA ← | curved DNA‑binding protein |
| RA | 1,238,197 | G→T | 7.7% | R209R (CGG→CGT) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,501,838 | G→T | 21.1% | D93Y (GAT→TAT) | tehB → | tellurite methyltransferase |
| RA | 1,558,568 | C→T | 7.1% | M150I (ATG→ATA) | ddpD ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD |
| RA | 1,579,498 | C→T | 5.5% | intergenic (‑156/‑47) | yddA ← / → yneP | ABC transporter family protein YddA/protein YneP |
| RA | 1,591,537 | C→A | 6.4% | G214W (GGG→TGG) | hipA ← | serine/threonine kinase HipA |
| RA | 1,642,447 | G→T | 10.8% | intergenic (+236/+42) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| JC | 1,705,265 | (CCACAACG)2→1 | 7.4% | coding (16‑23/441 nt) | ydgK → | conserved inner membrane protein YdgK |
| RA | 1,737,247 | A→G | 6.0% | F15S (TTT→TCT) | ydhP ← | putative transporter YdhP |
| RA | 1,756,860 | G→T | 8.9% | R388L (CGT→CTT) | pykF → | pyruvate kinase I |
| RA | 1,928,798 | A→T | 5.8% | L14L (CTT→CTA) | ptrB ← | oligopeptidase B |
| RA | 1,931,786 | G→T | 7.0% | L302L (CTG→CTT) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| RA | 1,945,170 | G→A | 8.9% | P63S (CCT→TCT) | ruvB ← | Holliday junction branch migration complex subunit RuvB |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,019,602 | A→G | 6.2% | intergenic (+89/‑16) | fliK → / → fliL | flagellar hook‑length control protein/flagellar protein FliL |
| 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 | 50.0% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,279 | C→A | 22.4% | intergenic (‑75/+233) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,190,665 | A→T | 5.4% | C82* (TGT→TGA) | yehB ← | putative fimbrial usher protein YehB |
| RA | 2,255,223 | C→A | 21.1% | intergenic (‑37/‑132) | rihB ← / → yeiL | pyrimidine‑specific ribonucleoside hydrolase RihB/putative DNA‑binding transcriptional regulator YeiL |
| RA | 2,395,451 | A→G | 7.0% | L149P (CTC→CCC) | nuoJ ← | NADH:quinone oxidoreductase subunit J |
| RA | 2,398,597 | G→A | 7.8% | R523R (CGC→CGT) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,449,031 | A→T | 6.3% | T142T (ACA→ACT) | smrB → | putative endonuclease SmrB |
| RA | 2,470,441 | C→A | 38.7% | D437E (GAC→GAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,444 | T→A | 38.7% | N438K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,506,970 | C→T | 7.4% | A309T (GCT→ACT) | fryC ← | putative PTS enzyme IIC component FryC |
| RA | 3,019,347 | A→T | 7.3% | N63Y (AAC→TAC) | ssnA → | putative aminohydrolase |
| RA | 3,140,231 | A→C | 19.1% | W30G (TGG→GGG) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,330,694 | T→A | 23.2% | D354V (GAT→GTT) | obgE ← | GTPase ObgE |
| RA | 3,394,325 | T→C | 6.4% | K645R (AAA→AGA) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,418,500 | T→A | 26.9% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,454,069 | G→T | 18.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,482,564 | G→C | 21.7% | E426Q (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 | 3,580,931 | G→T | 91.1% | noncoding (86/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,609,355 | T→G | 12.0% | F47V (TTT→GTT) | yhhQ → | putative queuosine precursor transporter |
| RA | 3,635,732 | A→G | 5.0% | T298A (ACC→GCC) | yhiM → | inner membrane protein with a role in acid resistance |
| RA | 3,749,095 | C→T | 6.4% | T173T (ACC→ACT) | sgbH → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase SgbH |
| RA | 3,750,302 | C→A | 7.8% | P73T (CCC→ACC) | sgbE → | L‑ribulose‑5‑phosphate 4‑epimerase SgbE |
| RA | 3,823,198 | G→A | 5.3% | V267I (GTC→ATC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,828,979 | A→C | 30.9% | Q12P (CAA→CCA) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,985 | T→G | 27.7% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,901,578 | T→A | 5.3% | T215S (ACC→TCC) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,955,638 | T→G | 23.2% | V103G (GTG→GGG) | ilvA → | threonine deaminase |
| RA | 3,976,613 | T→A | 5.2% | N112K (AAT→AAA) | wzxE → | lipid III flippase |
| RA | 4,127,839 | C→T | 10.1% | W19* (TGG→TAG) | yiiX ← | putative lipid binding hydrolase |
| RA | 4,147,657 | T→G | 23.6% | T221P (ACG→CCG) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,182,820 | C→T | 10.9% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,182,929 | A→T | 72.9% | E562V (GAA→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,283,228 | T→G | 54.9% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 32.0% | 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 | 4,399,799 | C→T | 6.7% | T183M (ACG→ATG) | miaA → | tRNA dimethylallyltransferase |
| RA | 4,580,043 | G→A | 5.5% | intergenic (+132/+25) | symR → / ← hsdS | small regulatory RNA SymR/type I restriction enzyme EcoKI specificity protein |
| RA | 4,581,441 | C→T | 5.9% | E8K (GAG→AAG) | hsdS ← | type I restriction enzyme EcoKI specificity protein |
| RA | 4,628,991 | A→T | 5.5% | I511N (ATT→AAT) | ettA ← | energy‑dependent translational throttle protein EttA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1731229 | 1731479 | 251 | 21 [19] | [20] 22 | lhr | putative ATP‑dependent helicase Lhr |
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424546–3424239 | 6–778 | 25 [17] | [20] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 37 (0.560) | 45 (0.790) | 36/204 | NT | 62.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 23 (0.400) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 37 (0.560) | 26 (0.450) | 22/204 | NT | 48.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 23 (0.400) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 70 (1.090) | 45/228 | 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 | 4542682 = | 46 (0.690) | 5 (0.080) | 5/218 | NT | 7.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 82 (1.340) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 45 (0.680) | 4 (0.070) | 4/218 | NT | 6.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 82 (1.340) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||