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_002947_CJ‑RC | 4,158,466 | 0 | T | G | 54.2% | 3.5 / 23.1 | 24 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.4% | 31.6 / 161.5 | 118 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.2% | ‑0.8 / 24.7 | 25 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.0% | 20.7 / 125.0 | 82 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 47.9% | 15.9 / 129.0 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 45.8% | 4.4 / 10.4 | 24 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 45.5% | 3.3 / 12.5 | 37 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 33.3% | 29.7 / 20.9 | 24 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 33.3% | 29.7 / 17.6 | 22 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,544,359 | 0 | C | G | 31.2% | 59.0 / 12.0 | 32 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 4,242,229 | 0 | T | G | 31.2% | 85.3 / 11.3 | 48 | D203A (GAC→GCC) | PP_3719 | putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 30.4% | 22.9 / 21.1 | 24 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 29.3% | 60.3 / 10.9 | 43 | T140A (ACC→GCC) | PP_1551 | replication protein O |
| * | NC_002947_CJ‑RC | 2,282,774 | 0 | G | C | 29.2% | 32.1 / 19.5 | 24 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,433,580 | 0 | G | C | 27.7% | 87.0 / 18.9 | 47 | intergenic (‑29/‑89) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,821,395 | 0 | G | . | 25.0% | 32.8 / 10.1 | 17 | intergenic (‑64/‑327) | PP_2474/PP_2475 | glutathione S‑transferase family protein/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 248,861 | 0 | C | A | 24.6% | 140.4 / 13.3 | 57 | Q148K (CAA→AAA) | PP_0198 | putative transporter |
| * | NC_002947_CJ‑RC | 1,898,657 | 0 | T | G | 23.8% | 99.9 / 10.7 | 42 | intergenic (+63/‑108) | PP_t16/PP_t17 | tRNA‑Asp/tRNA‑Val |
| * | NC_002947_CJ‑RC | 1,544,365 | 0 | T | G | 21.9% | 57.2 / 10.6 | 32 | V390G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 3,207,679 | 0 | G | C | 21.4% | 94.1 / 11.2 | 42 | S443T (AGC→ACC) | PP_2812 | transporter |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 19 (0.320) +GCC |
15/286 | 3.9 | 90.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 48 (0.780) | 12 (0.230) | 9/252 | 5.0 | 36.7% | 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 | = 5991572 | 56 (0.910) | 8 (0.140) | 8/276 | 5.9 | 14.3% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991794 = | 43 (0.740) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 55 (0.900) | 7 (0.120) | 7/276 | 6.3 | 14.1% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 33 (0.570) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 5126790 = | 44 (0.720) | 5 (0.100) | 5/240 | 6.5 | 14.9% | intergenic (+61/‑121) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease |
| ? | NC_002947_CJ‑RC | 5126869 = | 21 (0.420) | intergenic (+140/‑42) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease | |||||
| * | ? | NC_002947_CJ‑RC | = 4552080 | 11 (0.180) | 4 (0.080) | 4/226 | 6.7 | 26.2% | intergenic (+67/+114) | pydA/rutR | NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family |
| ? | NC_002947_CJ‑RC | = 4552131 | 14 (0.300) | intergenic (+118/+63) | pydA/rutR | NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family | |||||
| * | ? | NC_002947_CJ‑RC | 5916972 = | 29 (0.470) | 4 (0.080) | 4/236 | 6.9 | 18.4% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | 5917068 = | 12 (0.240) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 7 (0.120) +CGGG |
6/284 | 6.9 | 100% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 28 (0.460) | 6 (0.100) | 6/282 | 6.9 | 17.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 29 (0.490) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1419549 = | 26 (0.420) | 4 (0.080) | 3/234 | 7.5 | 18.3% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 1419637 = | 15 (0.310) | intergenic (‑126/+10) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||