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 | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 200,642 | C→T | 11.6% | A54V (GCC→GTC) | skp → | periplasmic chaperone Skp |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 909,422 | G→A | 33.3% | A543V (GCC→GTC) | poxB ← | pyruvate oxidase |
| RA | 987,560 | G→C | 12.9% | intergenic (‑578/+25) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 987,561 | G→C | 12.8% | intergenic (‑579/+24) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,026,927 | A→T | 100% | V30E (GTG→GAG) | mgsA ← | methylglyoxal synthase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,410,990 | T→A | 5.3% | intergenic (+106/+23) | dbpA → / ← ttcA | ATP‑dependent RNA helicase DbpA/tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| RA | 1,410,991 | T→A | 6.2% | intergenic (+107/+22) | dbpA → / ← ttcA | ATP‑dependent RNA helicase DbpA/tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| RA | 1,426,178 | A→T | 6.0% | intergenic (+198/‑276) | ydaY → / → ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,466,201 | T→C | 11.4% | pseudogene (810/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,708,973 | T→C | 20.3% | A685A (GCT→GCC) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,940,584 | C→A | 100% | R351L (CGT→CTT) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,941,326 | C→T | 100% | D104N (GAT→AAT) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,956,975 | G→T | 100% | H11Q (CAC→CAA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,306,277 | A→G | 18.7% | L160L (TTG→CTG) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,416,239 | C→T | 100% | T498M (ACG→ATG) | pta → | phosphate acetyltransferase |
| RA | 2,750,073 | G→T | 10.2% | intergenic (+13/+42) | yfjD → / ← grpE | putative inner membrane protein/nucleotide exchange factor GrpE |
| RA | 3,024,339 | A→G | 12.9% | intergenic (+153/‑12) | xdhD → / → xanQ | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit/xanthine:H(+) symporter XanQ |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,486,157 | A→C | 100% | E13A (GAA→GCA) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,959,515 | T→A | 5.9% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase (NADP(+))/peptidyl‑prolyl cis‑trans isomerase C |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,049,986 | G→T | 11.2% | noncoding (88/109 nt) | spf → | small regulatory RNA Spot 42 |
| RA | 4,049,989 | A→C | 11.1% | noncoding (91/109 nt) | spf → | small regulatory RNA Spot 42 |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,189,525 | C→G | 5.1% | S1392R (AGC→AGG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,196,219 | A→C | 6.6% | intergenic (‑120/+113) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 26.2% | 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 | 4,424,465 | G→T | 5.3% | intergenic (+79/+51) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| RA | 4,424,468 | A→C | 6.4% | intergenic (+82/+48) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196203 | 1211456 | 15254 | 15 [13] | [13] 14 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423754–3424519 | 3424519 | 1–766 | 16 [12] | [13] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3621183–3622359 | 3653153–3652030 | 29672–31971 | 14 [13] | [13] 14 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 274334 | NA (NA) | 5 (0.120) | 4/252 | NT | NA | noncoding (816/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274338 | NA (NA) | noncoding (812/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 5 (0.110) | 5/264 | NT | 13.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 674024 = | 33 (0.760) | coding (760/2583 nt) | leuS | leucine‑‑tRNA ligase | |||||
| * | ? | NC_000913 | = 899775 | NA (NA) | 4 (0.100) | 4/250 | NT | NA | noncoding (20/29 nt) | other | REPv82b |
| ? | NC_000913 | = 899786 | NA (NA) | noncoding (9/29 nt) | other | REPv82b | |||||
| * | ? | NC_000913 | 984434 = | NA (NA) | 3 (0.070) | 3/250 | NT | NA | noncoding (26/29 nt) | other | REPv86b |
| ? | NC_000913 | 984459 = | NA (NA) | noncoding (1/29 nt) | other | REPv86b | |||||
| * | ? | NC_000913 | 1310621 = | 45 (1.030) | 7 (0.160) | 7/264 | NT | 15.2% | coding (245/297 nt) | yciI | protein YciI |
| ? | NC_000913 | = 1517349 | 33 (0.760) | intergenic (‑155/‑40) | yncL/ortT | uncharacterized protein YncL/orphan toxin OrtT | |||||
| * | ? | NC_000913 | = 1785522 | 29 (0.670) | 3 (0.070) | 3/256 | NT | 9.2% | coding (1591/2379 nt) | ppsA | phosphoenolpyruvate synthetase |
| ? | NC_000913 | = 1785546 | 31 (0.730) | coding (1567/2379 nt) | ppsA | phosphoenolpyruvate synthetase | |||||
| * | ? | NC_000913 | 3185770 = | 39 (0.900) | 4 (0.100) | 3/254 | NT | 9.7% | coding (357/552 nt) | ygiL | putative fimbrial protein YgiL |
| ? | NC_000913 | 3185787 = | 37 (0.880) | coding (374/552 nt) | ygiL | putative fimbrial protein YgiL | |||||