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 25 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 | 66.7% | 50.0 / 32.8 | 30 | 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 | 63.0% | 26.8 / 31.8 | 30 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 57.9% | ‑3.1 / 14.6 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,353,290 | 0 | C | G | 55.6% | 2.3 / 10.1 | 9 | G103G (GGC→GGG) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 55.0% | ‑3.3 / 12.0 | 23 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 54.3% | 6.4 / 121.5 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.0% | 14.7 / 139.9 | 102 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 47.9% | 98.3 / 227.9 | 165 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 39.0% | 51.4 / 18.8 | 41 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 38.6% | 63.8 / 12.1 | 44 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 36.8% | 22.4 / 10.1 | 41 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 2,954,653 | 0 | A | G | 35.7% | 28.9 / 10.2 | 29 | intergenic (‑156/‑125) | PP_2586/PP_2587 | putative amino acid transporter/LuxR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 3,171,774 | 0 | A | T | 34.3% | 29.6 / 12.7 | 35 | I16F (ATT→TTT) | PP_2784 | short‑chain dehydrogenase/reductase family oxidoreductase |
| * | NC_002947_CJ‑RC | 1,403,591 | 0 | T | C | 28.6% | 18.5 / 10.5 | 25 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 6,048,001 | 0 | A | C | 27.9% | 84.6 / 10.8 | 43 | V35G (GTG→GGG) | PP_5297 | amino acid transporter |
| * | NC_002947_CJ‑RC | 131,262 | 0 | C | T | 27.0% | 121.2 / 46.2 | 74 | K4K (AAG→AAA) | engB | GTP‑binding protein |
| * | NC_002947_CJ‑RC | 3,516,064 | 0 | A | C | 26.9% | 93.0 / 11.8 | 52 | intergenic (+104/‑1031) | PP_5576/PP_5578 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 26.1% | 32.6 / 10.8 | 23 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,578,433 | 0 | G | T | 25.7% | 66.3 / 11.2 | 35 | intergenic (+110/‑214) | PP_3158/PP_5589 | hypothetical protein/rhs repeat‑associated core domain‑containing protein |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 25.6% | 108.5 / 36.7 | 44 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| Marginal new junction evidence (lowest skew 10 of 33 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 48 (0.690) | 12 (0.200) | 11/250 | 6.2 | 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 | = 2957080 | 35 (0.510) | 12 (0.180) | 12/280 | 6.7 | 26.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 34 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 9 (0.150) | 9/250 | 7.1 | 30.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 39 (0.650) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 11 (0.160) +GCC |
11/284 | 7.2 | 84.9% | 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 | = 4586136 | 9 (0.130) | 14 (0.220) | 9/268 | 7.6 | 49.7% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 20 (0.310) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 4 (0.060) | 11 (0.160) +CGGG |
9/282 | 8.0 | 73.9% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 4 (0.060) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.090) | 8 (0.150) | 5/220 | 8.3 | 29.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 33 (0.630) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472140 | 33 (0.480) | 4 (0.080) | 4/212 | 8.6 | 17.7% | intergenic (+44/+105) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | = 2472186 | 13 (0.260) | intergenic (+90/+59) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 5384101 = | 26 (0.380) | 4 (0.080) | 3/220 | 9.7 | 20.7% | intergenic (+18/+115) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | 5384199 = | 11 (0.210) | intergenic (+116/+17) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | = 5701558 | 22 (0.320) | 4 (0.070) | 4/256 | 10.1 | 17.6% | intergenic (+33/‑134) | hslU/PP_5002 | protease HslVU ATPase subunit/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 5701607 | 18 (0.290) | intergenic (+82/‑85) | hslU/PP_5002 | protease HslVU ATPase subunit/hypothetical protein | |||||