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 44 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 | 76.6% | 105.5 / 33.8 | 47 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 88.9% | 23.3 / ‑2.7 | 9 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 88.9% | 23.2 / ‑2.7 | 9 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 74.4% | 97.0 / 33.0 | 47 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.7% | 29.9 / 198.8 | 143 | 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 | 51.0% | 77.5 / 304.6 | 204 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.8% | ‑1.8 / 167.7 | 120 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 48.4% | 6.0 / 24.0 | 38 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 648,237 | 0 | T | G | 41.9% | 6.7 / 16.4 | 31 | intergenic (+6/+85) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 38.1% | 56.9 / 11.7 | 44 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 37.8% | 30.2 / 12.8 | 45 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,544,489 | 0 | C | A | 37.5% | 19.5 / 15.5 | 16 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,492 | 0 | G | C | 37.5% | 18.9 / 14.7 | 16 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,494 | 0 | C | G | 37.5% | 20.0 / 17.6 | 16 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,499 | 0 | C | G | 37.5% | 20.6 / 15.1 | 16 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,501 | 0 | G | C | 37.5% | 19.6 / 15.7 | 16 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 37.5% | 12.8 / 18.5 | 16 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 35.7% | 23.1 / 22.6 | 30 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 35.4% | 31.9 / 14.0 | 51 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,114,352 | 0 | G | T | 33.3% | 50.0 / 10.0 | 30 | intergenic (‑238/+28) | rluB/PP_4497 | 23S rRNA pseudouridylate synthase B/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 58 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 18 (0.200) +GCC |
16/284 | 7.2 | 94.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 20 (0.230) +CGGG |
14/282 | 7.8 | 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 | 4809877 = | 8 (0.090) | 12 (0.180) | 8/220 | 8.4 | 31.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 46 (0.670) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 37 (0.410) | 12 (0.140) | 12/280 | 8.5 | 22.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 47 (0.540) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 57 (0.630) | 11 (0.130) | 11/274 | 8.8 | 16.7% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 56 (0.660) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 17 (0.190) | 8 (0.090) | 8/276 | 10.2 | 30.7% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 20 (0.230) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 1487035 | 31 (0.340) | 5 (0.070) | 5/230 | 10.5 | 20.2% | intergenic (+51/+79) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | = 1487065 | 15 (0.210) | intergenic (+81/+49) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947_CJ‑RC | = 5873104 | 20 (0.220) | 6 (0.080) | 5/232 | 10.6 | 26.7% | intergenic (+50/+84) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator |
| ? | NC_002947_CJ‑RC | = 5873139 | 17 (0.240) | intergenic (+85/+49) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator | |||||
| * | ? | NC_002947_CJ‑RC | 5164273 = | 20 (0.220) | 5 (0.070) | 5/238 | 10.8 | 25.4% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947_CJ‑RC | 5164357 = | 13 (0.180) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 9 (0.100) | 9 (0.110) +CGGCGCTTCGCGG |
6/264 | 11.0 | 25.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 4946919 = | 49 (0.540) | intergenic (+576/+222) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||