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 23 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 60.0% | ‑3.0 / 16.2 | 21 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 58.8% | ‑4.9 / 13.5 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 53.6% | 5.0 / 23.0 | 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.0% | 23.6 / 158.2 | 115 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.4% | 19.5 / 158.9 | 113 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,740,951 | 0 | C | G | 47.4% | 3.9 / 21.4 | 19 | intergenic (+81/+672) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 45.3% | 29.5 / 20.7 | 55 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 44.8% | 28.7 / 111.1 | 87 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 44.6% | 24.2 / 22.1 | 59 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,740,948 | 0 | T | A | 44.4% | 2.6 / 16.4 | 18 | intergenic (+78/+675) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 42.1% | 10.4 / 19.5 | 19 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 4,740,949 | 0 | T | A | 38.9% | 9.4 / 14.8 | 18 | intergenic (+79/+674) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 2,101,751 | 0 | A | C | 34.7% | 35.2 / 11.4 | 52 | L186R (CTG→CGG) | PP_1878 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 30.5% | 56.7 / 10.8 | 59 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,583,678 | 0 | G | . | 30.4% | 50.2 / 21.1 | 24 | intergenic (‑144/+27) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| * | NC_002947_CJ‑RC | 2,793,757 | 0 | T | G | 30.0% | 39.6 / 12.8 | 32 | intergenic (+66/+61) | PP_2445/PP_2446 | membrane protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 647,259 | 0 | T | G | 28.0% | 100.9 / 11.5 | 50 | G294G (GGT→GGG) | acoR | acetoin catabolism regulatory protein |
| * | NC_002947_CJ‑RC | 4,798,317 | 0 | G | C | 25.9% | 36.4 / 15.7 | 28 | intergenic (‑172/+46) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 337,816 | 1 | . | A | 23.5% | 44.2 / 14.9 | 17 | intergenic (‑66/+63) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,827 | 0 | T | . | 23.5% | 38.3 / 10.3 | 17 | intergenic (‑77/+52) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 36 (0.570) | 13 (0.210) | 12/282 | 5.5 | 28.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 31 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 2 (0.030) | 6 (0.130) | 6/222 | 6.5 | 22.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 41 (0.850) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 6009389 | 24 (0.380) | 5 (0.110) | 5/220 | 6.9 | 20.8% | intergenic (+42/+57) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947_CJ‑RC | = 6009401 | 20 (0.420) | intergenic (+54/+45) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 18 (0.280) | 8 (0.130) | 8/278 | 6.9 | 34.7% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 13 (0.220) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.050) | 8 (0.130) +GCC |
8/286 | 7.1 | 73.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.050) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 8 (0.140) | 7/268 | 7.1 | 27.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 42 (0.720) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 51 (0.810) | 8 (0.150) | 6/252 | 7.2 | 26.7% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4552080 | 18 (0.280) | 4 (0.080) | 4/226 | 7.7 | 21.7% | intergenic (+67/+114) | pydA/rutR | NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family |
| ? | NC_002947_CJ‑RC | = 4552131 | 15 (0.310) | intergenic (+118/+63) | pydA/rutR | NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family | |||||
| * | ? | NC_002947_CJ‑RC | = 5516082 | 15 (0.240) | 4 (0.080) | 4/240 | 8.1 | 20.3% | intergenic (+45/‑109) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 5516138 | 19 (0.370) | intergenic (+101/‑53) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 380855 | 25 (0.400) | 4 (0.080) | 4/246 | 8.2 | 17.8% | intergenic (+45/+64) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | = 380889 | 16 (0.300) | intergenic (+79/+30) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer | |||||