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 | 697,107 | 0 | T | G | 60.0% | 2.2 / 21.9 | 29 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 59.3% | 0.3 / 10.6 | 27 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,164,207 | 0 | A | C | 58.8% | 5.4 / 19.3 | 18 | intergenic (+27/+174) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 57.7% | ‑3.0 / 18.2 | 27 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 55.9% | 17.5 / 190.9 | 145 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 54.6% | ‑1.8 / 138.6 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,296,567 | 0 | G | T | 52.9% | 2.8 / 17.0 | 17 | intergenic (‑320/‑246) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 52.0% | 2.7 / 18.7 | 28 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,161,575 | 0 | G | C | 46.4% | 16.0 / 13.9 | 28 | R395G (CGG→GGG) | PP_4543 | hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 42.9% | 41.1 / 123.1 | 98 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,703,248 | 0 | A | G | 38.1% | 12.4 / 17.1 | 21 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 38.1% | 21.5 / 18.5 | 21 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,252 | 0 | C | T | 38.1% | 14.6 / 17.3 | 21 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 4,935,577 | 0 | T | G | 36.0% | 54.9 / 11.7 | 52 | Q192P (CAG→CCG) | flhF | flagellar biosynthesis protein FlhF |
| * | NC_002947_CJ‑RC | 4,049,907 | 0 | A | G | 31.6% | 16.3 / 12.2 | 22 | intergenic (+40/‑61) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 27.6% | 125.2 / 12.3 | 58 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 3,985,645 | 0 | A | C | 27.5% | 80.1 / 10.4 | 53 | intergenic (+74/‑79) | PP_3513/oplB | LysR family transcriptional regulator/5‑oxoprolinase B |
| * | NC_002947_CJ‑RC | 4,044,569 | 0 | A | C | 25.7% | 136.2 / 20.0 | 74 | V380G (GTG→GGG) | PP_3566 | MFS transporter |
| * | NC_002947_CJ‑RC | 4,433,570 | 0 | C | A | 25.4% | 152.2 / 22.3 | 67 | intergenic (‑19/‑99) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,316,198 | 0 | C | A | 24.2% | 172.4 / 12.2 | 69 | intergenic (+73/‑28) | PP_1148/PP_mr15 | hypothetical protein/P20 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 34 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 13 (0.170) | 16 (0.280) | 12/222 | 5.4 | 34.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 51 (0.890) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.030) | 13 (0.200) | 11/252 | 6.6 | 27.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 67 (1.030) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 12 (0.160) | 15 (0.210) | 13/278 | 6.6 | 52.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 16 (0.220) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 11 (0.150) +GCC |
11/286 | 7.5 | 78.9% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 3 (0.040) | 10 (0.140) +CGGG |
9/284 | 8.3 | 77.4% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 3 (0.040) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 39 (0.520) | 9 (0.120) | 9/282 | 8.3 | 18.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 43 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 16 (0.210) | 12 (0.160) | 9/286 | 8.4 | 40.2% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 20 (0.270) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 13 (0.170) | 6 (0.100) | 5/240 | 9.2 | 15.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 57 (0.920) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1967145 = | 33 (0.440) | 6 (0.100) | 4/226 | 9.4 | 22.9% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947_CJ‑RC | 1967241 = | 15 (0.260) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | = 1531731 | 18 (0.240) | 8 (0.110) | 6/278 | 9.7 | 26.2% | coding (145/630 nt) | PP_1344 | hypothetical protein |
| ? | NC_002947_CJ‑RC | 1531839 = | 28 (0.390) | coding (37/630 nt) | PP_1344 | hypothetical protein | |||||