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 | 46,026 | G→T | 9.3% | G74C (GGT→TGT) | yaaU → | putative transporter YaaU |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 325,516 | C→T | 9.0% | intergenic (‑152/+61) | ykgH ← / ← betA | uncharacterized protein YkgH/choline dehydrogenase |
| RA | 488,818 | T→G | 27.4% | R761R (CGT→CGG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 569,071 | A→T | 7.3% | H57L (CAT→CTT) | ybcK → | DLP12 prophage; putative recombinase |
| RA | 752,065 | G→A | 11.8% | D35D (GAC→GAT) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 858,825 | G→T | 13.4% | R79R (CGC→CGA) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 960,443 | Δ1 bp | 10.3% | coding (180/765 nt) | ycaL → | periplasmic protease YcaL |
| RA | 977,596 | A→T | 12.9% | N424I (AAT→ATT) | mukB → | chromosome partitioning protein MukB |
| RA | 983,303 | C→T | 12.1% | R77C (CGC→TGC) | ycbK → | DUF882 domain‑containing protein YcbK |
| RA | 1,023,307 | C→A | 20.7% | E193* (GAA→TAA) | yccS ← | putative transporter YccS |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,395,423 | A→T | 10.5% | F167Y (TTC→TAC) | ynaI ← | small conductance mechanosensitive channel YnaI |
| RA | 1,645,046 | G→A | 8.7% | intergenic (‑144/+73) | rem ← / ← hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| RA | 1,894,192 | A→T | 7.6% | P20P (CCA→CCT) | yoaC → | DUF1889 domain‑containing protein YoaC |
| RA | 1,894,208 | A→T | 7.4% | N26Y (AAT→TAT) | yoaC → | DUF1889 domain‑containing protein YoaC |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,114,417 | A→T | 8.9% | intergenic (‑90/+85) | galF ← / ← wcaM | UTP:glucose‑1‑phosphate uridylyltransferase, low activity/putative colanic acid biosynthesis protein WcaM |
| RA | 2,167,169 | T→A | 7.3% | noncoding (56/87 nt) | cyaR → | small regulatory RNA CyaR |
| 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 | 57.6% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,272 | T→A | 21.8% | intergenic (‑68/+240) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,216,876 | T→C | 8.5% | T178A (ACG→GCG) | yehX ← | glycine betaine ABC transporter ATP binding subunit YehX |
| RA | 2,314,196 | G→T | 19.5% | D237Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,470,463 | G→T | 41.7% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,653,904 | G→A | 7.8% | noncoding (50/304 nt) | ryfA → | small regulatory RNA RyfA |
| RA | 2,666,379 | T→C | 10.1% | S315S (TCT→TCC) | csiE → | stationary phase inducible protein CsiE |
| RA | 2,843,243 | T→A | 8.0% | E68D (GAA→GAT) | hycH ← | formate hydrogenlyase assembly protein |
| RA | 2,887,806 | Δ1 bp | 12.9% | coding (507/735 nt) | cysH ← | phosphoadenosine phosphosulfate reductase |
| RA | 2,935,015 | C→T | 8.3% | R261C (CGC→TGC) | fucP → | L‑fucose:H(+) symporter |
| RA | 3,119,484 | A→G | 6.9% | intergenic (‑372/+113) | yghJ ← / ← glcA | putative lipoprotein YghJ/glycolate/lactate:H(+) symporter GlcA |
| RA | 3,152,204 | A→T | 14.3% | intergenic (‑220/‑32) | exbB ← / → metC | Ton complex subunit ExbB/cystathionine beta‑lyase/L‑cysteine desulfhydrase |
| RA | 3,221,341 | Δ1 bp | 10.3% | intergenic (‑94/‑125) | ygjH ← / → ebgR | putative tRNA‑binding protein YgjH/DNA‑binding transcriptional repressor EbgR |
| RA | 3,230,979 | G→A | 8.0% | G698S (GGC→AGC) | ygjK → | glycoside hydrolase |
| RA | 3,379,435 | C→T | 9.4% | R188H (CGT→CAT) | zapE ← | cell division factor ZapE with ATPase activity |
| MC JC | 3,384,721 | Δ435 bp | 100% | coding (19‑453/471 nt) | argR → | DNA‑binding transcriptional dual regulator ArgR |
| RA | 3,454,069 | G→T | 25.0% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,467,104 | C→A | 13.7% | intergenic (‑113/+56) | bfd ← / ← chiA | bacterioferritin‑associated ferredoxin/endochitinase |
| RA | 3,486,145 | A→C | 18.2% | D9A (GAC→GCC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,657,521 | C→T | 8.5% | A176V (GCC→GTC) | hdeD → | acid‑resistance membrane protein |
| RA | 3,733,965 | A→G | 9.1% | E82E (GAA→GAG) | xylH → | xylose ABC transporter membrane subunit |
| RA | 3,800,767 | T→A | 48.1% | K67* (AAG→TAG) | waaY ← | lipopolysaccharide core heptose (II) kinase |
| RA | 3,828,980 | A→C | 40.7% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,838,282 | T→A | 11.5% | L12Q (CTG→CAG) | yicL → | putative inner membrane protein |
| RA | 3,990,260 | A→G | 9.5% | L169L (CTT→CTC) | hemC ← | hydroxymethylbilane synthase |
| RA | 4,018,822 | T→A | 12.2% | intergenic (+62/‑33) | rmuC → / → ubiE | putative recombination limiting protein RmuC/bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase and S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,136,368 | G→C | 10.6% | A87A (GCG→GCC) | yijE → | cystine exporter |
| RA | 4,182,929 | A→T | 100% | E562V (GAA→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,951 | C→A | 13.4% | H17N (CAT→AAT) | nudC → | NADH pyrophosphatase |
| RA | 4,283,228 | T→G | 46.6% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 27.3% | 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 | 4,363,142 | A→C | 11.1% | L56R (CTT→CGT) | yjdC ← | putative DNA‑binding transcriptional regulator YjdC |
| RA | 4,407,648 | T→A | 9.2% | M332K (ATG→AAG) | rnr → | RNase R |
| RA | 4,446,975 | T→A | 12.2% | I955N (ATC→AAC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,521,412 | G→A | 9.7% | D203D (GAC→GAT) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,543,639 | G→A | 10.5% | A175A (GCG→GCA) | fimA → | type 1 fimbriae major subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 164549 | 164614 | 66 | 9 [4] | [7] 11 | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | * | ÷ | NC_000913 | 3423773–3424234 | 3424539–3424238 | 5–767 | 8 [7] | [6] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.650) | 17 (0.580) | 15/204 | NT | 50.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 14 (0.480) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.590) | 12 (0.410) | 12/204 | NT | 43.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 14 (0.480) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||