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_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0% | 11.5 / NA | 5 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0% | 11.5 / NA | 5 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 53.3% | ‑5.9 / 11.4 | 16 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.9% | ‑4.1 / 74.7 | 56 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 47.5% | 74.4 / 163.9 | 121 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 44.8% | 6.9 / 15.6 | 32 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 42.2% | 61.7 / 111.7 | 90 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 37.5% | 19.9 / 12.4 | 32 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 31.6% | 144.8 / 90.8 | 114 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 26.3% | 26.2 / 14.0 | 19 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 24.7% | 177.2 / 75.7 | 100 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 22.9% | 200.0 / 84.9 | 105 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,743,289 | 0 | C | A | 22.7% | 49.5 / 10.9 | 22 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 22.5% | 130.9 / 38.2 | 71 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 22.0% | 201.2 / 59.9 | 109 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 20.9% | 166.6 / 46.5 | 91 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 13 (0.240) | 18 (0.340) | 16/274 | 3.2 | 54.0% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 18 (0.340) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 34 (0.620) | 13 (0.280) | 11/240 | 3.9 | 47.2% | 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 | = 4809882 | 8 (0.150) | 12 (0.240) | 11/256 | 4.2 | 28.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 53 (1.060) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 8 (0.150) | 9 (0.190) | 8/240 | 4.9 | 24.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 50 (1.070) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5290126 | 17 (0.310) | 6 (0.140) | 6/220 | 5.3 | 27.7% | intergenic (‑104/+80) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | = 5290160 | 18 (0.420) | intergenic (‑138/+46) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 8 (0.150) +GCC |
8/274 | 5.5 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 5596907 = | 21 (0.380) | 4 (0.090) | 4/224 | 6.4 | 20.6% | intergenic (‑39/+106) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947_CJ‑RC | 5597000 = | 14 (0.320) | intergenic (‑132/+13) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947_CJ‑RC | 4809876 = | 6 (0.110) | 7 (0.130) | 6/276 | 6.4 | 23.8% | intergenic (‑282/‑273) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 4947075 | 39 (0.720) | intergenic (+732/+66) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947_CJ‑RC | 2540161 = | 62 (1.130) | 4 (0.080) | 4/268 | 7.3 | 6.4% | intergenic (‑22/‑93) | PP_2231/PP_2232 | DMT superfamily permease/XRE family transcriptional regulator |
| ? | NC_002947_CJ‑RC | 2540179 = | 57 (1.090) | intergenic (‑40/‑75) | PP_2231/PP_2232 | DMT superfamily permease/XRE family transcriptional regulator | |||||
| * | ? | NC_002947_CJ‑RC | 1034215 = | 61 (1.110) | 4 (0.080) | 4/270 | 7.3 | 6.5% | coding (252/1158 nt) | PP_0892 | phospholipase family protein |
| ? | NC_002947_CJ‑RC | 1034236 = | 56 (1.060) | coding (273/1158 nt) | PP_0892 | phospholipase family protein | |||||