mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 345,428 | T→C | 16.3% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 444,779 | C→T | 61.6% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 982,560 | T→A | 100% | intergenic (‑122/+481) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,466,255 | C→A | 65.0% | pseudogene (1482/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 2,217,123 | A→G | 19.0% | Y487C (TAC→TGC) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 54.3% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,419,720 | T→C | 37.5% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,353 | A→G | 68.6% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,506,454 | C→T | 28.5% | intergenic (‑269/‑67) | mntH ← / → nupC | manganese/divalent cation transporter/nucleoside (except guanosine) transporter |
| RA | 2,707,318 | A→G | 12.0% | H355R (CAT→CGT) | srmB → | ATP‑dependent RNA helicase |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 40.0% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,371,135 | G→T | 29.3% | intergenic (‑356/+39) | sspA ← / ← rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 |
| RA | 3,528,506 | A→C | 50.1% | V241G (GTA→GGA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,536,804 | T→C | 13.7% | F93F (TTT→TTC) | yhgA → | transposase_31 family protein |
| RA | 3,600,471 | G→A | 12.9% | A221T (GCC→ACC) | zntA → | zinc, cobalt and lead efflux system |
| RA | 3,676,832 | G→T | 100% | intergenic (‑25/+158) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| JC | 3,676,860:1 | (GGTACCTGCGG)1→2 | 95.2% | intergenic (‑53/+130) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,742,902 | C→T | 5.6% | A104V (GCG→GTG) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 224595 | NA (NA) | 3 (0.120) | 3/268 | NT | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | = 224611 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 39 (1.460) | 36/276 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1045234 = | 27 (1.010) | 23 (0.860) | 18/276 | NT | 52.9% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 14 (0.530) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 1 (0.040) | 13 (0.550) | 12/244 | NT | 93.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 1 (0.040) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 1 (0.040) | 11 (0.470) | 11/244 | NT | 92.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 1 (0.040) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1973115 = | 16 (0.600) | 15 (0.560) | 15/276 | NT | 48.4% | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2096424 | NA (NA) | 38 (1.430) | 32/276 | NT | 65.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2427745 | 20 (0.750) | coding (476/660 nt) | dedA | DedA family inner membrane protein | |||||
| * | ? | CP009273 | = 2686693 | 21 (0.790) | 4 (0.160) | 3/264 | NT | 15.4% | coding (2210/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase |
| ? | CP009273 | = 2686756 | 24 (0.940) | coding (2147/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase | |||||
| * | ? | CP009273 | 3274911 = | 34 (1.280) | 3 (0.120) | 3/264 | NT | 8.4% | pseudogene (482/555 nt) | agaA | pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase |
| ? | CP009273 | 3274929 = | 33 (1.300) | pseudogene (500/555 nt) | agaA | pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase | |||||