mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| JC | 70,406 | Δ6 bp | 70.0% | coding (20‑25/879 nt) | araC → | ara regulon transcriptional activator; autorepressor |
| RA | 100,839 | C→T | 11.7% | V25V (GTC→GTT) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 922,314:1 | +C | 5.7% | intergenic (+21/+52) | macB → / ← cspD | macrolide ABC transporter peremase/ATPase/inhibitor of DNA replication, cold shock protein homolog |
| RA | 924,050 | T→G | 28.2% | F263V (TTT→GTT) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,036,090 | G→A | 5.4% | A107A (GCG→GCA) | hyaD → | hydrogenase 1 maturation protease |
| JC JC | 1,198,576 | IS2 (–) +5 bp | 23.3% | intergenic (‑339/‑115) | ymfE ← / → lit | e14 prophage; putative inner membrane protein/T4 phage exclusion protein; cell death peptidase, e14 prophage |
| RA | 1,810,065 | T→G | 5.5% | intergenic (+17/‑146) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,066 | C→A | 5.0% | intergenic (+18/‑145) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,173,497 | G→A | 84.2% | pseudogene (782/914 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 | 2,938,327 | G→A | 10.5% | C287Y (TGC→TAC) | fucK → | L‑fuculokinase |
| RA | 2,939,592 | C→A | 80.9% | S75R (AGC→AGA) | fucR → | l‑fucose operon activator |
| RA | 2,939,611 | G→T | 17.4% | D82Y (GAT→TAT) | fucR → | l‑fucose operon activator |
| RA | 2,962,561 | G→A | 5.7% | N68N (AAC→AAT) ‡ | ppdC ← | putative prepilin peptidase‑dependent protein |
| RA | 2,962,562 | T→C | 5.7% | N68S (AAC→AGC) ‡ | ppdC ← | putative prepilin peptidase‑dependent protein |
| RA | 2,976,321 | C→A | 5.6% | noncoding (65/82 nt) | omrB ← | sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent |
| RA | 3,371,068 | A→G | 5.2% | intergenic (‑32/+16) | nanE ← / ← nanT | putative N‑acetylmannosamine‑6‑P epimerase/sialic acid transporter |
| RA | 3,541,500 | C→T | 29.7% | S365F (TCC→TTC) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| 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 |
| JC | 3,815,859 | Δ82 bp | 50.3% | [rph]–[rph] | [rph], [rph] | |
| RA | 4,148,049 | C→G | 5.3% | G90A (GGC→GCC) | yijO ← | AraC family putative transcriptional activator |
| RA | 4,215,883 | C→T | 29.3% | L136L (CTG→TTG) | aceB → | malate synthase A |
| RA | 4,296,190 | A→G | 19.3% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 20.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 28.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 15.5% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423789–3424537 | 3424537 | 1–749 | 62 [61] | [61] 62 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 62 (0.490) | 46 (0.390) | 41/532 | NT | 46.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 49 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 63 (0.500) | 55 (0.460) | 51/532 | NT | 50.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 49 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 166 (1.340) | 136/556 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1411899 = | 127 (1.010) | 13 (0.110) | 13/512 | NT | 10.5% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 107 (0.940) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 30 (0.240) | 30/564 | NT | 16.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4079792 | 156 (1.240) | coding (42/219 nt) | yiiF | putative thymol sensitivity protein, CopG family putative transcriptional regulator | |||||
| * | ? | NC_000913 | 3781698 = | NA (NA) | 3 (0.020) | 3/550 | NT | NA | noncoding (1/29 nt) | REP273 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP273 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 3781727 = | NA (NA) | intergenic (+39/+14) | trmL/cysE | tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent/serine acetyltransferase | |||||