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 | 44,734 | G→A | 9.3% | V185V (GTG→GTA) | fixC → | putative oxidoreductase FixC |
| RA | 190,863 | G→T | 8.4% | E3* (GAA→TAA) | tsf → | protein chain elongation factor EF‑Ts |
| RA | 238,497 | G→T | 20.7% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 21.6% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 28.4% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 41.3% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 263,910 | C→T | 5.5% | R33Q (CGG→CAG) | yafW ← | antitoxin of the YkfI‑YafW toxin‑antitoxin pair |
| RA | 310,966 | C→A | 23.1% | R124I (AGA→ATA) | ecpR ← | DNA‑binding transcriptional dual regulator MatA |
| RA | 380,841 | A→G | 8.9% | M1T (ATG→ACG) † | yaiO ← | outer membrane protein YaiO |
| RA | 420,079 | T→A | 9.3% | S163S (TCT→TCA) | brnQ → | branched chain amino acid transporter BrnQ |
| RA | 481,400 | C→T | 8.9% | A1002T (GCA→ACA) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 845,954 | T→C | 11.8% | E170E (GAA→GAG) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 891,421 | T→C | 10.5% | C80R (TGT→CGT) | nfsA → | NADPH‑dependent nitroreductase NfsA |
| RA | 1,076,477 | T→G | 21.2% | K802N (AAA→AAC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,145,247 | Δ1 bp | 12.1% | coding (308/960 nt) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,145,248 | Δ1 bp | 12.5% | coding (309/960 nt) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,145,249 | Δ1 bp | 12.5% | coding (310/960 nt) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,145,250 | Δ1 bp | 12.5% | coding (311/960 nt) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,235,131 | A→T | 8.0% | H65L (CAT→CTT) | fadR → | DNA‑binding transcriptional dual regulator FadR |
| RA | 1,328,932 | C→T | 7.5% | G61R (GGG→AGG) | yciK ← | putative oxidoreductase |
| RA | 1,343,304 | T→G | 16.4% | T9P (ACC→CCC) | osmB ← | osmotically‑inducible lipoprotein OsmB |
| RA | 1,549,261 | G→T | 11.0% | E621* (GAA→TAA) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,569,713 | G→A | 11.5% | V259V (GTC→GTT) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,592,765 | A→T | 5.6% | pseudogene (5322/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,641,262 | C→A | 15.1% | intergenic (‑677/+77) | essQ ← / ← cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock‑like protein CspB |
| RA | 1,865,154 | A→G | 11.1% | C161C (TGT→TGC) | yeaE ← | methylglyoxal reductase YeaE |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,145,946 | T→A | 8.9% | L894H (CTT→CAT) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,155,113 | A→T | 13.8% | A366A (GCA→GCT) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| 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 | 64.3% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 60.5% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,314,181 | G→T | 20.8% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,314,196 | G→T | 24.7% | D237Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,340,753 | C→T | 10.2% | Q1139Q (CAG→CAA) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,456,871 | G→C | 26.2% | intergenic (‑59/+144) | sixA ← / ← fadJ | phosphohistidine phosphatase/3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,470,431 | G→T | 34.7% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 37.4% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,721,930 | G→A | 10.0% | V660I (GTT→ATT) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,904,387 | C→T | 6.5% | intergenic (+1013/+360) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 3,050,194 | T→A | 10.2% | T158T (ACA→ACT) | gcvT ← | aminomethyltransferase |
| RA | 3,142,403 | T→C | 8.2% | E196G (GAG→GGG) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,177,414 | A→T | 10.8% | I166N (ATT→AAT) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,305,425 | A→C | 14.7% | G131G (GGT→GGG) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,411,035 | G→A | 6.0% | L252L (TTG→TTA) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,421,159 | C→T | 8.2% | P342P (CCC→CCT) | yhdX → | putative ABC transporter membrane subunit YhdX |
| RA | 3,532,847 | A→T | 8.3% | Q10H (CAA→CAT) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,609,760 | G→A | 6.8% | D182N (GAT→AAT) | yhhQ → | putative queuosine precursor transporter |
| RA | 3,633,501 | G→A | 6.8% | pseudogene (958/1607 nt) | yhiL ← | putative uncharacterized protein YhiL |
| RA | 3,662,593 | T→C | 8.0% | V727A (GTG→GCG) | mdtF → | multidrug efflux pump RND permease MdtF |
| JC | 3,815,859 | Δ82 bp | 47.2% | [rph] | [rph] | |
| RA | 3,828,979 | A→C | 46.8% | Q12P (CAA→CCA) ‡ | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,980 | A→C | 34.9% | Q12H (CAA→CAC) ‡ | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,985 | T→G | 39.4% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 4,026,774 | A→G | 8.3% | K83R (AAA→AGA) | fre → | flavin reductase |
| RA | 4,120,810 | G→A | 7.0% | A313V (GCG→GTG) | hslU ← | ATPase component of the HslVU protease |
| MC JC | 4,123,449 | Δ990 bp | 100% | coding (19‑1008/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 23.2% | 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 | 4,375,764 | C→T | 8.5% | Y22Y (TAC→TAT) | efp → | protein chain elongation factor EF‑P |
| RA | 4,378,560 | T→C | 6.2% | T129A (ACT→GCT) | ampC ← | beta‑lactamase |
| RA | 4,392,554 | G→T | 44.9% | intergenic (+7/‑29) | glyX → / → glyY | tRNA‑Gly/tRNA‑Gly |
| RA | 4,446,528 | A→T | 8.5% | N806I (AAC→ATC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,602,509 | C→A | 7.3% | W117L (TGG→TTG) | yjjP ← | putative succinate exporter YjjP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423759–3424234 | 3424546–3424238 | 5–788 | 14 [12] | [13] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.440) | 37 (0.910) | 25/204 | NT | 69.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 15 (0.370) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 19 (0.400) | 16 (0.390) | 15/204 | NT | 50.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 15 (0.370) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 53 (1.160) | 33/228 | 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 | |||||