mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 1,070,246 | 2 | . | A | 63.6% | 27.1 / 25.6 | 23 | 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 | 61.9% | 33.9 / 24.5 | 23 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 60.3% | 4.0 / 144.9 | 127 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.0% | 10.4 / 138.5 | 100 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 50.0% | 21.5 / 16.7 | 33 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,161,575 | 0 | G | C | 46.4% | 27.8 / 12.4 | 28 | R395G (CGG→GGG) | PP_4543 | hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 44.7% | 31.2 / 121.9 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 44.1% | 12.0 / 11.9 | 34 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 40.6% | 11.1 / 10.5 | 33 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 955,149 | 0 | A | G | 36.8% | 13.3 / 15.3 | 19 | intergenic (+103/‑210) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,155 | 0 | C | T | 35.0% | 20.2 / 13.7 | 20 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,151 | 0 | G | A | 33.3% | 23.3 / 13.9 | 21 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,152 | 0 | T | A | 33.3% | 22.0 / 16.6 | 21 | intergenic (+106/‑207) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,153 | 0 | T | C | 33.3% | 20.3 / 15.2 | 21 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 3,975,989 | 0 | T | G | 33.3% | 73.6 / 17.7 | 48 | P293P (CCA→CCC) | PP_3506 | magnesium chelatase subunit ChII |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 33.3% | 19.0 / 10.5 | 15 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 25.7% | 129.1 / 41.2 | 70 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 24.2% | 47.5 / 17.8 | 33 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,530,127 | 1 | . | G | 23.5% | 28.6 / 14.6 | 17 | intergenic (+26/‑142) | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 22.6% | 82.1 / 20.4 | 31 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| Marginal new junction evidence (lowest skew 10 of 42 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 1 (0.020) | 15 (0.310) | 11/220 | 4.2 | 54.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 24 (0.500) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 51 (0.800) | 8 (0.130) | 8/274 | 6.6 | 17.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 27 (0.450) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 25 (0.390) | 8 (0.130) | 8/280 | 6.7 | 20.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 37 (0.600) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1487006 = | 27 (0.420) | 5 (0.100) | 5/230 | 7.0 | 26.0% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | 1487096 = | 7 (0.140) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947_CJ‑RC | = 2282748 | 35 (0.550) | 7 (0.110) | 7/278 | 7.1 | 20.4% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 21 (0.340) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 9 (0.140) +GCC |
7/284 | 7.3 | 82.1% | 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 | 1499507 = | 4 (0.060) | 6 (0.100) | 6/266 | 7.3 | 15.2% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 63 (1.080) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 7 (0.110) | 7 (0.110) | 7/284 | 7.3 | 31.2% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 24 (0.380) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 51 (0.800) | 7 (0.130) | 5/250 | 7.5 | 24.1% | 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 | = 4809882 | 0 (0.000) | 6 (0.100) | 5/266 | 7.9 | 19.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 51 (0.870) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||