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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 389,919:1 | +T | 100% | intergenic (‑192/‑332) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,108,708 | A→T | 15.4% | Y78* (TAT→TAA) | opgC ← | OPG biosynthetic transmembrane succinyltransferase |
| RA | 1,158,559 | C→T | 77.8% | Q231* (CAG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC | 1,158,725 | Δ96 bp | 32.8% | coding (857‑952/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,219,420 | G→A | 10.6% | intergenic (+219/‑181) | ymgF → / → ycgH | inner membrane division septum protein/pseudogene; putative ATP‑binding component of a transport system |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,544,021:1 | +A | 75.9% | coding (40/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,544,022 | C→A | 100% | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| RA | 1,726,165 | A→G | 23.5% | Y48C (TAC→TGC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,433 | Δ11 bp | 38.3% | coding (411‑421/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,757,058 | G→C | 16.7% | G454A (GGT→GCT) | pykF → | pyruvate kinase I |
| RA | 1,774,576 | G→A | 100% | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 2,976,638 | T→G | 58.0% | S14A (TCA→GCA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 2,977,096 | Δ1 bp | 19.4% | coding (498/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,946,711 | C→A | 15.6% | noncoding (12/120 nt) | rrfC → | 5S ribosomal RNA of rrnC operon |
| RA | 4,183,136 | G→T | 57.7% | R637L (CGT→CTT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,183,195 | A→T | 25.1% | T657S (ACC→TCC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,207,558 | A→G | 11.5% | intergenic (‑44/‑571) | purH ← / → rrsE | IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon |
| RA | 4,296,042 | C→T | 31.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,362:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,698 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_hsa_tpiA | 365916 | 366431 | 516 | 8 [7] | [7] 8 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423750–3424234 | 3424535–3424239 | 6–786 | 8 [7] | [7] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 5 (0.150) | 12 (0.420) | 12/244 | NT | 60.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 11 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 7 (0.220) | 12 (0.420) | 11/244 | NT | 58.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 11 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3216668 = | 45 (1.390) | 3 (0.100) | 3/262 | NT | 7.1% | noncoding (68/78 nt) | REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_hsa_tpiA | = 4614265 | 36 (1.170) | noncoding (27/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||