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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,596,055 | 0 | T | G | 66.7% | 29.0 / 18.2 | 24 | pseudogene (1933/3861 nt) | yneO | pseudogene, AidA homolog |
| * | NC_000913 | 238,527 | 0 | A | G | 46.2% | 3.0 / 49.7 | 39 | I70I (ATT→ATC) | ykfM | lethality reduction protein, putative inner membrane protein |
| * | NC_000913 | 757,179 | 0 | G | T | 40.0% | 8.2 / 13.7 | 15 | E425* (GAG→TAG) | sdhA | succinate dehydrogenase, flavoprotein subunit |
| * | NC_000913 | 4,296,060 | 0 | C | T | 34.9% | 45.1 / 37.9 | 43 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,196,220 | 0 | C | T | 33.3% | 30.0 / 20.0 | 27 | H366H (CAC→CAT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,232 | 0 | C | T | 33.3% | 29.8 / 20.0 | 27 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 763,895 | 0 | C | G | 30.3% | 50.9 / 26.3 | 33 | T294T (ACC→ACG) | sucC | succinyl‑CoA synthetase, beta subunit |
| * | NC_000913 | 3,781,051 | 0 | C | G | 26.5% | 52.0 / 23.0 | 34 | intergenic (+34/‑164) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 2,753,986 | 0 | A | T | 21.1% | 77.9 / 15.3 | 38 | intergenic (+40/+22) | bamE/ratB | lipoprotein component of BamABCDE OM biogenesis complex/UPF0125 family protein |
| * | NC_000913 | 657,531 | 0 | T | G | 20.6% | 67.2 / 15.7 | 34 | intergenic (+30/+24) | cspE/flc | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 657,533 | 0 | A | T | 20.6% | 69.5 / 12.0 | 34 | intergenic (+32/+22) | cspE/flc | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 317,566 | 0 | G | A | 20.0% | 85.2 / 14.6 | 41 | pseudogene (128/129 nt) | ykgQ | pseudogene, putative dehydrogenase |
| * | NC_000913 | 657,535 | 0 | C | A | 20.0% | 75.3 / 11.5 | 35 | intergenic (+34/+20) | cspE/flc | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 3,334,704 | 0 | G | C | 20.0% | 93.3 / 20.5 | 40 | intergenic (+23/‑205) | ispB/sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| * | NC_000913 | 3,334,705 | 0 | C | T | 20.0% | 85.4 / 11.4 | 40 | intergenic (+24/‑204) | ispB/sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1999548 | 40 (1.230) | 8 (0.260) | 6/238 | 3.0 | 16.8% | intergenic (‑68/+37) | dcyD/fliY | D‑cysteine desulfhydrase, PLP‑dependent/cystine transporter subunit |
| ? | NC_000913 | = 1999563 | 42 (1.380) | intergenic (‑83/+22) | dcyD/fliY | D‑cysteine desulfhydrase, PLP‑dependent/cystine transporter subunit | |||||
| * | ? | NC_000913 | = 521828 | 31 (0.960) | 6 (0.200) | 6/236 | 3.0 | 18.0% | coding (1413/2415 nt) | ybbP | putative ABC transporter permease |
| ? | NC_000913 | = 521858 | 26 (0.860) | coding (1443/2415 nt) | ybbP | putative ABC transporter permease | |||||
| * | ? | NC_000913 | = 2787809 | 32 (0.990) | 6 (0.190) | 6/254 | 3.2 | 15.8% | pseudogene (1413/2253 nt) | ygaQ | uncharacterized protein; putative enzyme |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1049778 = | NA (NA) | 6 (0.190) | 6/254 | 3.2 | 15.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2787809 | 32 (0.990) | pseudogene (1413/2253 nt) | ygaQ | uncharacterized protein; putative enzyme | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 6 (0.190) | 6/254 | 3.2 | 15.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2787809 | 32 (0.990) | pseudogene (1413/2253 nt) | ygaQ | uncharacterized protein; putative enzyme | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 5 (0.170) | 5/236 | 3.3 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3922214 = | 50 (1.540) | 5 (0.160) | 5/244 | 3.4 | 9.4% | coding (227/381 nt) | atpI | ATP synthase, membrane‑bound accessory factor |
| ? | NC_000913 | 3922243 = | 48 (1.540) | coding (198/381 nt) | atpI | ATP synthase, membrane‑bound accessory factor | |||||
| * | ? | NC_000913 | 1359446 = | 26 (0.800) | 6 (0.190) | 5/242 | 3.4 | 18.2% | intergenic (‑259/+44) | puuP/puuA | putrescine importer/glutamate‑‑putrescine ligase |
| ? | NC_000913 | 1359466 = | 29 (0.940) | intergenic (‑279/+24) | puuP/puuA | putrescine importer/glutamate‑‑putrescine ligase | |||||
| * | ? | NC_000913 | = 398608 | 33 (1.020) | 5 (0.160) | 5/240 | 3.4 | 13.9% | coding (737/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein |
| ? | NC_000913 | = 398612 | 31 (1.010) | coding (741/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein | |||||
| * | ? | NC_000913 | = 4297512 | 37 (1.140) | 4 (0.130) | 4/238 | 3.7 | 10.3% | coding (1855/2148 nt) | fdhF | formate dehydrogenase‑H, selenopolypeptide subunit |
| ? | NC_000913 | = 4297530 | 35 (1.150) | coding (1837/2148 nt) | fdhF | formate dehydrogenase‑H, selenopolypeptide subunit | |||||