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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,302,452 | 0 | A | C | 33.3% | 26.6 / 19.3 | 24 | L101R (CTG→CGG) | napA | nitrate reductase, periplasmic, large subunit |
| * | NC_000913 | 987,560 | 0 | G | C | 30.8% | 35.6 / 20.3 | 26 | intergenic (‑578/+25) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 987,561 | 0 | G | C | 30.8% | 34.1 / 22.2 | 26 | intergenic (‑579/+24) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| * | NC_000913 | 1,987,857 | 0 | C | T | 30.0% | 38.3 / 18.1 | 30 | intergenic (‑99/+16) | yecJ/azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| * | NC_000913 | 1,987,858 | 0 | G | C | 30.0% | 44.7 / 26.0 | 30 | intergenic (‑100/+15) | yecJ/azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| * | NC_000913 | 1,987,859 | 0 | G | C | 30.0% | 43.5 / 26.2 | 30 | intergenic (‑101/+14) | yecJ/azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| * | NC_000913 | 1,987,860 | 0 | A | G | 30.0% | 37.4 / 20.1 | 30 | intergenic (‑102/+13) | yecJ/azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| * | NC_000913 | 4,213,131 | 0 | C | T | 27.6% | 37.4 / 16.6 | 29 | noncoding (92/120 nt) | rrfE | 5S ribosomal RNA of rrnE operon |
| * | NC_000913 | 3,811,218 | 0 | G | C | 27.3% | 56.4 / 24.7 | 33 | intergenic (‑66/+32) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.7% | 46.1 / 17.2 | 30 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 2,305,086 | 0 | C | G | 25.0% | 50.1 / 18.0 | 28 | intergenic (+693/+22) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 2,305,087 | 0 | C | T | 25.0% | 44.9 / 12.3 | 28 | intergenic (+694/+21) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 3,811,219 | 0 | A | G | 25.0% | 51.1 / 16.7 | 32 | intergenic (‑67/+31) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 3,811,223 | 0 | A | G | 25.0% | 52.5 / 16.0 | 32 | intergenic (‑71/+27) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 3,811,212 | 0 | C | T | 24.2% | 56.0 / 14.5 | 33 | intergenic (‑60/+38) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 3,811,216 | 0 | C | T | 24.2% | 56.7 / 15.8 | 33 | intergenic (‑64/+34) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 3,811,217 | 0 | G | C | 24.2% | 64.0 / 22.2 | 33 | intergenic (‑65/+33) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| * | NC_000913 | 2,305,085 | 0 | A | G | 24.1% | 45.9 / 12.7 | 29 | intergenic (+692/+23) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 2,375,483 | 0 | A | T | 23.3% | 53.6 / 14.9 | 30 | L160L (CTT→CTA) ‡ | menC | O‑succinylbenzoyl‑CoA synthase |
| * | NC_000913 | 2,375,484 | 0 | A | T | 23.3% | 54.0 / 14.8 | 30 | L160H (CTT→CAT) ‡ | menC | O‑succinylbenzoyl‑CoA synthase |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3587430 = | 28 (0.970) | 6 (0.230) | 6/232 | 2.5 | 18.8% | coding (684/744 nt) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic |
| ? | NC_000913 | 3587464 = | 26 (0.980) | coding (650/744 nt) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic | |||||
| * | ? | NC_000913 | 2700550 = | 31 (1.070) | 5 (0.200) | 5/214 | 2.6 | 17.8% | noncoding (31/77 nt) | ohsC | sRNA antisense regulator of shoB toxin |
| ? | NC_000913 | 2700601 = | 20 (0.820) | intergenic (+5/+17) | ohsC/acpS | sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1 | |||||
| * | ? | NC_000913 | 2258692 = | 28 (0.970) | 6 (0.210) | 6/244 | 2.6 | 18.7% | coding (605/942 nt) | psuK | pseudouridine kinase |
| ? | NC_000913 | 2258736 = | 25 (0.890) | coding (561/942 nt) | psuK | pseudouridine kinase | |||||
| * | ? | NC_000913 | = 4369155 | 29 (1.010) | 4 (0.150) | 4/232 | 3.1 | 14.6% | intergenic (+15/+1) | fxsA/yjeH | suppressor of F exclusion of phage T7/putative transporter |
| ? | NC_000913 | = 4369174 | 20 (0.750) | coding (1239/1257 nt) | yjeH | putative transporter | |||||
| * | ? | NC_000913 | 2139570 = | 35 (1.210) | 4 (0.150) | 4/230 | 3.1 | 11.8% | intergenic (+85/+189) | yegH/asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| ? | NC_000913 | 2139603 = | 28 (1.060) | intergenic (+118/+156) | yegH/asmA | inner membrane protein/suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein | |||||
| * | ? | NC_000913 | 1823325 = | NA (NA) | 4 (0.150) | 4/232 | 3.1 | NA | intergenic (+40/‑190) | nadE/cho | NAD synthetase, NH3/glutamine‑dependent/endonuclease of nucleotide excision repair |
| ? | NC_000913 | 1823349 = | NA (NA) | noncoding (19/98 nt) | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP130 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 671548 = | 31 (1.070) | 4 (0.150) | 4/230 | 3.1 | 12.6% | coding (58/1032 nt) | holA | DNA polymerase III, delta subunit |
| ? | NC_000913 | 671580 = | 27 (1.030) | coding (26/1032 nt) | holA | DNA polymerase III, delta subunit | |||||
| * | ? | NC_000913 | = 3780085 | 33 (1.140) | 4 (0.150) | 4/234 | 3.2 | 13.2% | coding (259/1191 nt) | lldD | L‑lactate dehydrogenase, FMN‑linked |
| ? | NC_000913 | = 3780114 | 22 (0.820) | coding (288/1191 nt) | lldD | L‑lactate dehydrogenase, FMN‑linked | |||||
| * | ? | NC_000913 | = 3659757 | 29 (1.010) | 4 (0.150) | 4/240 | 3.2 | 14.4% | coding (526/1158 nt) | mdtE | anaerobic multidrug efflux transporter, ArcA‑regulated |
| ? | NC_000913 | = 3659790 | 20 (0.730) | coding (559/1158 nt) | mdtE | anaerobic multidrug efflux transporter, ArcA‑regulated | |||||
| * | ? | NC_000913 | 3643087 = | 22 (0.760) | 4 (0.150) | 4/236 | 3.2 | 14.9% | coding (46/753 nt) | rsmJ | 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3643107 = | 25 (0.930) | coding (26/753 nt) | rsmJ | 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent | |||||