mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,529,175 | T→C | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,560,455 | +G | 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 | 4,070,814 | G→A | R315C (CGT→TGT) | yihS ← | sulphoquinovose isomerase |
| RA | 4,070,817 | C→A | V314L (GTA→TTA) | yihS ← | sulphoquinovose isomerase |
| RA | 4,075,135 | T→G | I156S (ATC→AGC) | yihW → | putative transcriptional regulator for sulphoquinovose utilization |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 384711 | 385093 | 383 | 50 [49] | [49] 52 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 2469008 | 2470794 | 1787 | 52 [47] | [48] 50 | [gtrB]–gtrS | [gtrB],gtrS |
| * | * | ÷ | NC_000913 | 2785832 | 2786702 | 871 | 53 [47] | [46] 50 | [ileY]–[ygaQ] | [ileY],[ygaQ] |
| * | * | ÷ | NC_000913 | 2884176 | 2884540 | 365 | 50 [49] | [49] 52 | casA/ygcB | CRISP RNA (crRNA) containing Cascade antiviral complex protein/Cascade complex anti‑viral R‑loop helicase‑annealase Cas3 |
| * | * | ÷ | NC_000913 | 2993342 | 2994401 | 1060 | 51 [49] | [34] 53 | [ygeH]–[pbl] | [ygeH],ygeI,pbl,[pbl] |
| * | * | ÷ | NC_000913 | 3267923 | 3269664 | 1742 | 53 [48] | [44] 50 | [yhaB]–yhaC | [yhaB],yhaC |
| * | * | ÷ | NC_000913 | 3499158 | 3499531 | 374 | 50 [49] | [49] 50 | [cysG]–[yhfL] | [cysG],[yhfL] |
| * | * | ÷ | NC_000913 | 4541516 | 4542064 | 549 | 50 [49] | [49] 50 | [fimB]–[fimE] | [fimB],[fimE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 13 (0.100) | 77 (0.640) | 53/498 | 1.0 | 84.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.140) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.100) | 104 (0.860) | 68/498 | 0.3 | 87.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.140) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 515 (4.010) | 187/530 | 0.0 | 80.1% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3844640 | 128 (1.000) | coding (677/1767 nt) | adeD | cryptic adenine deaminase | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 534 (4.160) | 185/530 | 0.0 | 81.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3712115 = | 119 (0.930) | intergenic (‑108/+121) | yhjX/yhjY | pyruvate‑inducible inner membrane protein, putative transporter/autotransporter beta‑domain protein | |||||
| * | ? | NC_000913 | 3836116 = | 190 (1.480) | 109 (0.850) | 79/530 | 0.2 | 36.4% | intergenic (‑187/‑106) | yicJ/selC | putative transporter/tRNA‑Sec |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||