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 |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 380,012 | 1 | . | G | 59.7% | 264.7 / 222.6 | 129 | intergenic (‑131/+57) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| * | NC_000913 | 937,372 | 0 | A | G | 54.5% | 53.4 / 229.7 | 178 | M1M (ATG→GTG) † | lolA | lipoprotein chaperone |
| * | NC_000913 | 2,755,880 | 0 | G | A | 54.3% | 479.9 / inf | 1407 | intergenic (+502/‑279) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase |
| * | NC_000913 | 986,848 | 0 | A | G | 53.9% | 113.4 / inf | 508 | F45F (TTT→TTC) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,863 | 0 | A | G | 51.5% | 46.8 / inf | 507 | V40V (GTT→GTC) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 4,148,010 | 0 | C | A | 48.7% | 43.1 / inf | 234 | G103V (GGC→GTC) | yijO | AraC family putative transcriptional activator |
| * | NC_000913 | 986,023 | 0 | G | A | 40.9% | 244.6 / inf | 375 | G320G (GGC→GGT) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 1,744,981 | 0 | T | C | 39.6% | 119.2 / 197.7 | 177 | T383A (ACC→GCC) | ydhQ | autotransporter adhesin‑related protein |
| * | NC_000913 | 3,946,246 | 0 | G | A | 39.2% | 236.4 / 266.4 | 247 | noncoding (2543/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913 | 3,461,324 | 0 | A | G | 37.1% | 191.8 / 248.4 | 240 | D101G (GAT→GGT) | gspG | pseudopilin, cryptic, general secretion pathway |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.1% | 534.8 / 305.0 | 375 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 986,566 | 0 | T | C | 28.2% | 449.1 / 231.5 | 309 | E139E (GAA→GAG) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,569 | 0 | T | A | 28.1% | 569.6 / 235.6 | 307 | P138P (CCA→CCT) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,413 | 0 | A | G | 27.7% | 463.9 / 216.8 | 311 | R190R (CGT→CGC) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,560 | 0 | A | G | 25.7% | 436.8 / 165.7 | 263 | G141G (GGT→GGC) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,551 | 0 | A | C | 25.1% | 564.7 / 204.0 | 291 | T144T (ACT→ACG) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 986,554 | 0 | A | G | 24.6% | 516.9 / 170.2 | 284 | D143D (GAT→GAC) | ompF | outer membrane porin 1a (Ia;b;F) |
| * | NC_000913 | 3,822,554 | 0 | T | C | 22.8% | 405.7 / 121.0 | 219 | V52A (GTT→GCT) | spoT | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| * | NC_000913 | 4,534,184 | 0 | C | A | 22.6% | 472.9 / 133.6 | 208 | intergenic (‑131/+246) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment |
| Marginal new junction evidence (lowest skew 10 of 785 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 140 (1.260) +44 bp |
13/110 | 10.5 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382211 | NA (NA) | 58 (0.300) | 27/188 | 11.3 | NA | noncoding (952/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382218 | NA (NA) | noncoding (959/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2304648 | 76 (0.380) | 50 (0.250) | 24/194 | 12.7 | 21.2% | noncoding (232/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2305013 | 297 (1.510) | noncoding (597/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | = 4296054 | 389 (1.940) | 23 (0.190) +40 bp |
9/118 | 13.6 | 11.2% | noncoding (220/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913 | = 4628779 | 222 (1.110) | noncoding (85/150 nt) | RIP354 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP354 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 2894874 | NA (NA) | 23 (0.190) +40 bp |
9/118 | 13.6 | 9.0% | noncoding (67/67 nt) | REP201 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP201 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 4296054 | 389 (1.940) | noncoding (220/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | = 2066832 | 0 (0.000) | 34 (0.190) | 19/180 | 13.7 | 100% | noncoding (522/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2066857 | NA (NA) | noncoding (497/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3386201 | 218 (1.090) | 24 (0.130) | 18/176 | 13.8 | 11.3% | intergenic (‑72/+20) | yhcO/aaeB | putative barnase inhibitor/p‑hydroxybenzoic acid efflux system component |
| ? | NC_000913 | = 3386206 | 183 (1.030) | intergenic (‑77/+15) | yhcO/aaeB | putative barnase inhibitor/p‑hydroxybenzoic acid efflux system component | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 109 (0.580) | 19/186 | 14.1 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4296054 | 389 (1.940) | 23 (0.190) +40 bp |
8/118 | 14.2 | 9.0% | noncoding (220/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913 | = 4614644 | NA (NA) | noncoding (388/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||
| * | ? | NC_000913 | 4229376 = | NA (NA) | 23 (0.190) +40 bp |
8/118 | 14.2 | 9.0% | noncoding (1/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 4296054 | 389 (1.940) | noncoding (220/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||