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 |
| Marginal read alignment evidence (highest frequency 20 of 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 3,342,312 | 0 | C | G | 45.5% | 2.1 / 12.7 | 11 | P14A (CCT→GCT) | kdsC | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| * | NC_000913_3_pae_pgi | 3,504,875 | 0 | T | G | 38.5% | ‑0.9 / 13.4 | 13 | intergenic (+92/+60) | frlR/yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| * | NC_000913_3_pae_pgi | 3,342,316 | 0 | T | A | 35.7% | 10.1 / 12.0 | 14 | V15D (GTC→GAC) | kdsC | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| * | NC_000913_3_pae_pgi | 2,724,095 | 0 | C | A | 35.3% | 17.8 / 14.2 | 17 | intergenic (+13/‑33) | pssA/yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| * | NC_000913_3_pae_pgi | 2,724,097 | 0 | T | A | 35.3% | 18.3 / 12.6 | 17 | intergenic (+15/‑31) | pssA/yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| * | NC_000913_3_pae_pgi | 2,724,099 | 0 | T | G | 35.3% | 10.3 / 17.3 | 17 | intergenic (+17/‑29) | pssA/yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| * | NC_000913_3_pae_pgi | 526,792 | 0 | A | C | 33.3% | 8.5 / 12.3 | 15 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 987,560 | 0 | G | C | 33.3% | 23.4 / 20.2 | 21 | intergenic (‑578/+25) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913_3_pae_pgi | 987,561 | 0 | G | C | 33.3% | 26.3 / 18.4 | 21 | intergenic (‑579/+24) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913_3_pae_pgi | 3,342,320 | 0 | C | G | 33.3% | 20.7 / 10.1 | 15 | S16R (AGC→AGG) | kdsC | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 31.8% | 22.3 / 15.2 | 22 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_pgi | 595,520 | 0 | T | A | 31.6% | 22.7 / 15.9 | 20 | intergenic (‑77/‑80) | cusR/cusC | response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component |
| * | NC_000913_3_pae_pgi | 595,519 | 0 | T | A | 30.0% | 25.9 / 15.8 | 20 | intergenic (‑76/‑81) | cusR/cusC | response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component |
| * | NC_000913_3_pae_pgi | 3,980,726 | 0 | G | A | 30.0% | 23.6 / 11.0 | 20 | intergenic (+30/‑161) | wecG/yifK | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter |
| * | NC_000913_3_pae_pgi | 3,980,727 | 0 | T | C | 30.0% | 24.7 / 11.3 | 20 | intergenic (+31/‑160) | wecG/yifK | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative APC family amino acid transporter |
| * | NC_000913_3_pae_pgi | 475,971 | 0 | C | G | 29.2% | 40.9 / 19.5 | 24 | intergenic (+20/+11) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| * | NC_000913_3_pae_pgi | 475,972 | 0 | C | G | 29.2% | 41.7 / 18.8 | 24 | intergenic (+21/+10) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| * | NC_000913_3_pae_pgi | 4,423,725 | 0 | G | T | 28.6% | 34.7 / 13.6 | 21 | intergenic (+79/+51) | ulaF/yjfY | L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic |
| * | NC_000913_3_pae_pgi | 4,423,728 | 0 | A | C | 28.6% | 25.4 / 16.1 | 21 | intergenic (+82/+48) | ulaF/yjfY | L‑ribulose 5‑phosphate 4‑epimerase/YhcN family protein, periplasmic |
| * | NC_000913_3_pae_pgi | 2,407,898 | 0 | A | C | 27.8% | 22.3 / 12.8 | 18 | Q113P (CAG→CCG) | alaA | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | 786795 = | 21 (1.300) | 4 (0.270) | 4/232 | 1.5 | 16.9% | intergenic (+110/+48) | aroG/gpmA | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible/phosphoglyceromutase 1 |
| ? | NC_000913_3_pae_pgi | 786822 = | 20 (1.340) | intergenic (+137/+21) | aroG/gpmA | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible/phosphoglyceromutase 1 | |||||
| * | ? | NC_000913_3_pae_pgi | = 3839138 | 21 (1.300) | 4 (0.260) | 4/236 | 1.6 | 15.5% | coding (891/924 nt) | yicL | EamA family inner membrane putative transporter |
| ? | NC_000913_3_pae_pgi | = 3839155 | 24 (1.580) | coding (908/924 nt) | yicL | EamA family inner membrane putative transporter | |||||
| * | ? | NC_000913_3_pae_pgi | 730508 = | 18 (1.110) | 4 (0.260) | 4/240 | 1.6 | 19.0% | coding (926/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913_3_pae_pgi | 730544 = | 17 (1.100) | coding (962/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913_3_pae_pgi | = 4533399 | 11 (0.680) | 3 (0.200) | 3/232 | 1.8 | 19.9% | intergenic (‑86/+291) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment |
| ? | NC_000913_3_pae_pgi | = 4533420 | 14 (0.940) | intergenic (‑107/+270) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment | |||||
| * | ? | NC_000913_3_pae_pgi | 2792954 = | 20 (1.230) | 3 (0.200) | 3/238 | 1.9 | 14.3% | coding (220/1281 nt) | gabT | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| ? | NC_000913_3_pae_pgi | 2793007 = | 17 (1.110) | coding (273/1281 nt) | gabT | 4‑aminobutyrate aminotransferase, PLP‑dependent | |||||
| * | ? | NC_000913_3_pae_pgi | 2286347 = | 14 (0.860) | 4 (0.260) | 3/236 | 1.9 | 22.8% | intergenic (+60/+43) | proL/yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| ? | NC_000913_3_pae_pgi | 2286381 = | 14 (0.920) | intergenic (+94/+9) | proL/yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913_3_pae_pgi | 2264074 = | 20 (1.230) | 3 (0.190) | 3/240 | 1.9 | 13.0% | coding (212/1182 nt) | setB | lactose/glucose efflux system |
| ? | NC_000913_3_pae_pgi | 2264102 = | 21 (1.360) | coding (240/1182 nt) | setB | lactose/glucose efflux system | |||||
| * | ? | NC_000913_3_pae_pgi | 390532 = | 13 (0.800) | 3 (0.190) | 3/240 | 1.9 | 19.8% | pseudogene (282/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| ? | NC_000913_3_pae_pgi | 390559 = | 12 (0.780) | pseudogene (309/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein | |||||