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 42 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 | 1,070,246 | 2 | . | A | 70.7% | 77.2 / 39.6 | 41 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 69.4% | 64.7 / 34.7 | 41 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 65.6% | 4.9 / 16.1 | 35 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 56.2% | ‑4.8 / 12.1 | 17 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 53.3% | ‑0.8 / 15.0 | 18 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.7% | 20.1 / 203.5 | 150 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 2,939,300 | 0 | C | A | 50.0% | 7.4 / 16.4 | 20 | intergenic (‑246/+194) | PP_2570/PP_2572 | transposase/hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 49.7% | 5.9 / 220.3 | 145 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 48.4% | ‑4.7 / 17.5 | 34 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 41.2% | 165.7 / 191.9 | 171 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 40.9% | 13.7 / 14.5 | 23 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 38.1% | 23.0 / 12.5 | 46 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 37.6% | 78.9 / 29.9 | 97 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,840,084 | 0 | T | G | 34.1% | 67.8 / 10.3 | 45 | intergenic (+16/+20) | PP_1646/PP_1647 | thioredoxin/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 31.6% | 127.0 / 18.6 | 76 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 30.8% | 107.6 / 17.9 | 66 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 30.2% | 84.4 / 24.0 | 94 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 29.2% | 142.5 / 67.9 | 89 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 26.9% | 90.7 / 17.9 | 52 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 6,094,964 | 0 | A | C | 26.9% | 119.5 / 16.1 | 67 | S192R (AGC→CGC) | PP_5343 | putative Transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 87 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.030) | 23 (0.250) +GCC |
21/286 | 5.7 | 88.7% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.040) | 15 (0.180) | 15/268 | 7.0 | 38.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 44 (0.520) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 81 (0.870) | 13 (0.160) | 13/252 | 7.2 | 27.1% | 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 | 4809877 = | 5 (0.050) | 19 (0.270) | 10/222 | 7.5 | 45.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 42 (0.600) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 39 (0.420) | 15 (0.170) | 14/282 | 7.7 | 28.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 37 (0.410) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.050) | 9 (0.120) | 6/240 | 10.2 | 29.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 40 (0.530) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1906682 = | 25 (0.270) | 5 (0.070) | 5/240 | 10.8 | 18.0% | intergenic (+22/+106) | nirD/PP_1707 | nitrite reductase/D‑isomer specific 2‑hydroxyacid dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 1906776 = | 25 (0.330) | intergenic (+116/+12) | nirD/PP_1707 | nitrite reductase/D‑isomer specific 2‑hydroxyacid dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 19 (0.210) | 7 (0.080) | 6/278 | 11.4 | 24.1% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 26 (0.290) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 2050595 | 31 (0.330) | 3 (0.040) | 3/218 | 11.5 | 11.1% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2050631 | 25 (0.360) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 6080636 = | 41 (0.440) | 4 (0.050) | 4/244 | 11.6 | 12.1% | intergenic (‑123/+115) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter |
| ? | NC_002947_CJ‑RC | 6080736 = | 24 (0.310) | intergenic (‑223/+15) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter | |||||