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 |
JC | 102,158 | +TGGTAATAT | 5.1% | coding (1394/1476 nt) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
RA | 526,792 | A→C | 6.6% | S1178R (AGC→CGC) | rhsD → | protein RhsD |
RA | 526,796 | C→G | 6.7% | A1179G (GCG→GGG) | rhsD → | protein RhsD |
RA | 872,805 | C→T | 7.6% | intergenic (+4/‑174) | gsiD → / → pdeI | glutathione ABC transporter membrane subunit GsiD/putative c‑di‑GMP phosphodiesterase PdeI |
RA | 1,529,175 | T→C | 8.5% | pseudogene (1286/2049 nt) | rhsE → | RhsE protein in rhs element |
RA | 1,529,180 | T→C | 8.3% | pseudogene (1291/2049 nt) | rhsE → | RhsE protein in rhs element |
RA | 1,529,185 | C→T | 8.6% | pseudogene (1296/2049 nt) | rhsE → | RhsE protein in rhs element |
RA | 1,529,203 | C→A | 12.7% | pseudogene (1314/2049 nt) | rhsE → | RhsE protein in rhs element |
RA | 1,529,218 | C→T | 16.9% | pseudogene (1329/2049 nt) | rhsE → | RhsE protein in rhs element |
RA | 1,708,758 | G→C | 9.7% | E614Q (GAA→CAA) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 3,505,145 | T→C | 5.7% | R292R (AGA→AGG) | yhfS ← | putative aminotransferase YhfS |
RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
RA | 3,815,809 | Δ1 bp | 6.7% | intergenic (‑41/+54) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
RA | 3,815,822 | T→G | 6.7% | intergenic (‑54/+41) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
RA | 3,815,937 | C→A | 7.3% | E205* (GAA→TAA) | rph ← | truncated RNase PH |
RA | 4,184,809 | G→T | 64.7% | G1189C (GGT→TGT) | rpoB → | RNA polymerase subunit beta |
RA | 4,296,190 | A→G | 20.6% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,296,191 | A→C | 23.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,296,268 | T→C | 10.4% | intergenic (+474/+168) | 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 | 4,566,266 | T→C | 5.3% | R327R (CGA→CGG) | yjiN ← | DUF445 domain‑containing protein YjiN |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 1207790 = | 84 (0.740) | 40 (0.380) | 31/462 | NT | 34.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | 1209619 = | 72 (0.680) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1207805 | 84 (0.740) | 55 (0.520) | 39/462 | NT | 42.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | = 1209602 | 72 (0.680) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 38 (0.340) | 34/486 | 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 | 2054966 = | 113 (1.000) | 6 (0.060) | 5/474 | NT | 5.5% | intergenic (+7/‑95) | shiA/amn | shikimate:H(+) symporter/AMP nucleosidase |
? | NC_000913 | 2054990 = | 99 (0.910) | intergenic (+31/‑71) | shiA/amn | shikimate:H(+) symporter/AMP nucleosidase | |||||
* | ? | NC_000913 | = 2515616 | NA (NA) | 7 (0.060) | 7/488 | NT | 5.4% | noncoding (1344/1345 nt) | IS186 | repeat region |
? | NC_000913 | 4543608 = | 122 (1.090) | coding (494/549 nt) | fimA | type 1 fimbriae major subunit |