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 | annotation | gene | description |
| RA | 12,854 | A→G | D231G (GAC→GGC) | dnaK → | chaperone protein DnaK |
| RA | 149,558 | (T)8→7 | coding (44/795 nt) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 166,503 | A→G | T592A (ACC→GCC) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 186,345 | A→G | V769A (GTT→GCT) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| RA | 188,603 | C→T | L16L (CTG→CTA) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| RA | 192,297 | C→T | A148V (GCA→GTA) | pyrH → | UMP kinase |
| RA | 255,127 | A→G | V197A (GTT→GCT) | pepD ← | peptidase D |
| RA | 265,534 | A→G | S4P (TCC→CCC) | ykfF ← | CP4‑6 prophage; protein YkfF |
| RA | 268,303 | T→C | S220G (AGC→GGC) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 282,008 | T→C | intergenic (‑25/‑270) | yagA ← / → yagE | CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 368,313 | C→T | L36L (CTG→CTA) | mhpR ← | DNA‑binding transcriptional activator MhpR |
| RA | 371,924 | C→T | A229V (GCG→GTG) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 509,589 | A→G | G597G (GGT→GGC) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 511,405 | A→G | intergenic (‑26/‑236) | copA ← / → glsA | Cu(+) exporting P‑type ATPase/glutaminase 1 |
| RA | 548,352 | T→C | intergenic (+5/‑5) | fdrA → / → ylbE | putative acyl‑CoA synthetase FdrA/DUF1116 domain‑containing protein YlbE |
| RA | 615,337 | T→A | I394N (ATC→AAC) | entF → | apo‑serine activating enzyme |
| RA | 739,292 | C→T | H98Y (CAC→TAC) | ybgA → | DUF1722 domain‑containing protein YbgA |
| RA | 811,946 | T→C | V142A (GTG→GCG) | bioC → | malonyl‑acyl carrier protein methyltransferase |
| RA | 838,617 | C→T | S197S (TCG→TCA) | ybiX ← | PKHD‑type hydroxylase YbiX |
| RA | 841,817 | A→G | G80G (GGT→GGC) | mcbA ← | DUF1471 domain‑containing protein McbA |
| RA | 1,001,732 | Δ1 bp | coding (2517/2601 nt) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,001,758 | A→G | E848G (GAG→GGG) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,057,412 | A→G | R181R (CGT→CGC) | torR ← | DNA‑binding transcriptional dual regulator TorR |
| RA | 1,077,367 | C→T | G506S (GGT→AGT) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,105,929 | C→T | A37V (GCC→GTC) | ymdB → | 2'‑O‑acetyl‑ADP‑ribose deacetylase, regulator of RNase III activity |
| RA | 1,142,262 | T→C | Q702Q (CAA→CAG) | rne ← | ribonuclease E |
| RA | 1,180,775 | A→G | Y165H (TAT→CAT) | ycfZ ← | putative inner membrane protein |
| RA | 1,213,728 | T→C | Y111C (TAC→TGC) | bluR ← | DNA‑binding transcriptional repressor BluR |
| RA | 1,250,624 | G→A | A72V (GCC→GTC) | dhaK ← | dihydroxyacetone kinase subunit K |
| RA | 1,285,129 | A→G | E509G (GAG→GGG) | narH → | nitrate reductase A subunit beta |
| RA | 1,319,172 | A→G | L206P (CTG→CCG) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,338,661 | T→C | E167G (GAA→GGA) | ribA ← | GTP cyclohydrolase 2 |
| RA | 1,351,196 | (G)7→6 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,363,299 | A→G | N186S (AAC→AGC) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,386,324 | A→G | S272G (AGC→GGC) | ycjF → | conserved inner membrane protein YcjF |
| RA | 1,403,542 | A→G | S342P (TCT→CCT) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,451,128 | A→G | G74G (GGT→GGC) | tynA ← | copper‑containing amine oxidase |
| RA | 1,503,977 | A→G | G87G (GGA→GGG) | insQ → | putative insertion element transposase InsQ |
| RA | 1,515,125 | A→G | T122A (ACC→GCC) | ydcV → | putative ABC transporter membrane subunit YdcV |
| RA | 1,594,256 | (C)8→7 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,653,270 | T→C | T216A (ACA→GCA) | rspB ← | putative zinc‑binding dehydrogenase RspB |
| RA | 1,662,532 | (A)6→5 | coding (1977/2424 nt) | ynfF → | putative selenate reductase YnfF |
| RA | 1,689,403 | T→C | G276G (GGT→GGC) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,703,755 | G→A | A185V (GCC→GTC) | ydgJ ← | putative oxidoreductase YdgJ |
| RA | 1,763,614 | A→G | V132V (GTT→GTC) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,769,478 | (G)7→8 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| RA | 1,806,042 | (C)6→7 | coding (42/759 nt) | ydiY ← | acid‑inducible putative outer membrane protein YdiY |
| RA | 1,850,117 | C→T | T427T (ACC→ACT) | sppA → | protease IV, a signal peptide peptidase |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,954,493 | A→G | intergenic (+80/+85) | cmoB → / ← torZ | tRNA U34 carboxymethyltransferase/trimethylamine N‑oxide reductase 2 |
| RA | 1,966,718 | G→A | A107V (GCC→GTC) | cheZ ← | chemotaxis protein CheZ |
| RA | 1,999,336 | C→T | G49S (GGC→AGC) | dcyD ← | D‑cysteine desulfhydrase |
| RA | 2,021,640 | +C | coding (137/366 nt) | fliO → | flagellar biosynthesis protein FliO |
| RA | 2,036,683 | T→C | G283G (GGT→GGC) | hchA → | protein/nucleic acid deglycase 1 |
| RA | 2,048,065 | T→C | V1043A (GTT→GCT) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,111,423 | G→A | A185V (GCG→GTG) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,115,056 | T→C | T281A (ACG→GCG) | wcaM ← | putative colanic acid biosynthesis protein WcaM |
| RA | 2,190,298 | +C | coding (613/2481 nt) | yehB ← | putative fimbrial usher protein YehB |
| RA | 2,219,201 | T→C | N94S (AAC→AGC) | osmF ← | glycine betaine ABC transporter periplasmic binding protein OsmF |
| RA | 2,262,915 | G→A | P194L (CCG→CTG) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | 2,302,032 | A→G | V241A (GTG→GCG) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,302,729 | T→C | M9V (ATG→GTG) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,326,966 | (C)6→5 | coding (858/1185 nt) | atoB → | acetyl‑CoA acetyltransferase |
| RA | 2,388,698 | A→G | T22A (ACT→GCT) | yfbO → | uncharacterized protein YfbO |
| RA | 2,466,064 | C→T | P255L (CCC→CTC) | yfdC → | inner membrane protein YfdC |
| RA | 2,487,207 | T→C | V945A (GTC→GCC) | evgS → | sensory histidine kinase EvgS |
| RA | 2,515,635 | (T)7→6 | intergenic (+192/+8) | insL‑3 → / ← pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA |
| RA | 2,523,807 | A→T | I60N (ATC→AAC) | xapB ← | xanthosine:H(+) symporter XapB |
| RA | 2,564,703 | A→G | R61G (AGA→GGA) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,613,731 | T→C | L611S (TTA→TCA) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,637,938 | T→C | T239A (ACC→GCC) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,652,203 | (T)6→7 | coding (85/4962 nt) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,686,141 | T→C | L103L (TTG→CTG) | hmp → | nitric oxide dioxygenase |
| RA | 2,759,073 | +C | coding (89/1410 nt) | yfjI → | CP4‑57 prophage; protein YfjI |
| RA | 2,808,348 | G→A | pseudogene (33/1178 nt) | ygaY → | putative transporter YgaY, N‑terminal fragment |
| RA | 2,819,910 | T→C | E701G (GAA→GGA) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,854,741 | G→A | C135Y (TGT→TAT) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | 2,951,417 | G→A | R349C (CGC→TGC) | recD ← | exodeoxyribonuclease V subunit RecD |
| RA | 2,961,288 | T→C | S381G (AGC→GGC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,964,957 | T→C | T67A (ACT→GCT) | thyA ← | thymidylate synthase |
| RA | 2,969,464 | C→T | E5K (GAA→AAA) | ygdT ← | hypothetical protein |
| RA | 2,999,755 | (C)6→7 | coding (137/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,032,427 | T→C | V354A (GTA→GCA) | uacT → | urate:H(+) symporter |
| RA | 3,052,058 | T→C | D87G (GAC→GGC) | ubiI ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,068,945 | G→A | intergenic (‑137/+2) | argO ← / ← mscS | L‑arginine exporter/small conductance mechanosensitive channel MscS |
| RA | 3,071,913 | T→C | D237G (GAC→GGC) | pgk ← | phosphoglycerate kinase |
| RA | 3,086,984 | G→A | L93L (CTG→CTA) | metK → | methionine adenosyltransferase |
| RA | 3,108,347 | T→C | D270G (GAC→GGC) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,138,410 | T→C | Y38C (TAC→TGC) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,269,695 | T→C | intergenic (+93/+521) | yhaC → / ← rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,397,340 | T→C | E152E (GAA→GAG) | rng ← | RNase G |
| RA | 3,401,818 | A→G | C505C (TGT→TGC) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,457,365 | T→C | V330A (GTC→GCC) | gspD → | Type II secretion system protein GspD |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,596,391 | (A)5→6 | coding (13/927 nt) | livH ← | branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH |
| RA | 3,812,525 | (T)6→5 | coding (35/669 nt) | yicR ← | RadC‑like JAB domain‑containing protein YicR |
| RA | 3,891,806 | T→C | R64R (CGT→CGC) | mdtL → | efflux pump MdtL |
| RA | 3,917,434 | T→C | T278A (ACC→GCC) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,941,433 | C→T | intergenic (‑106/‑375) | yieP ← / → rrsC | putative transcriptional regulator YieP/16S ribosomal RNA |
| RA | 3,980,959 | A→G | T25A (ACC→GCC) | yifK → | putative transporter YifK |
| RA | 4,250,699 | T→C | intergenic (+225/‑4) | malM → / → yjbI | maltose regulon periplasmic protein/pentapeptide repeats‑containing protein YjbI |
| RA | 4,268,487 | (T)7→8 | intergenic (+180/+322) | tyrB → / ← yjbS | tyrosine aminotransferase/uncharacterized protein YjbS |
| RA | 4,294,705 | A→G | K75K (AAA→AAG) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,369,968 | T→C | T149A (ACC→GCC) | yjeH ← | L‑methionine/branched chain amino acid exporter |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,450,243 | A→G | E94E (GAA→GAG) | ytfQ → | galactofuranose ABC transporter periplasmic binding protein |
| RA | 4,586,406 | T→C | Y119C (TAC→TGC) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,612,280 | A→G | K51K (AAA→AAG) | ytjA → | DUF1328 domain‑containing protein YtjA |
| RA | 4,617,260 | A→G | intergenic (‑195/‑63) | yjjI ← / → deoC | DUF3029 domain‑containing protein YjjI/deoxyribose‑phosphate aldolase |
| RA | 4,623,175 | G→T | L315M (CTG→ATG) | lplA ← | lipoate‑‑protein ligase A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361194 | 361919 | 726 | 192 [184] | [183] 186 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856989 | 2857095 | 107 | 186 [183] | [0] 308 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423679–3424234 | 3424614–3424238 | 5–936 | 186 [183] | [183] 187 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 277 (0.910) | 298 (1.020) | 153/190 | 0.1 | 69.0% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||