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 27 shown, sorted by frequency from high to low) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 55.0% | ‑6.4 / 19.5 | 24 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 55.0% | 3.4 / 24.5 | 20 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
* | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.1% | 7.9 / 168.8 | 128 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
* | NC_002947_CJ‑RC | 1,712,090 | 0 | G | C | 52.2% | 21.4 / 35.4 | 23 | intergenic (+81/‑177) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
* | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.5% | ‑0.9 / 134.1 | 97 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 50.7% | 57.5 / 213.1 | 144 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,809,890 | 0 | G | T | 50.0% | ‑2.2 / 12.9 | 10 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
* | NC_002947_CJ‑RC | 5,455,911 | 0 | G | T | 41.2% | 17.9 / 10.7 | 18 | intergenic (+109/‑246) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
* | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 38.2% | 28.1 / 17.0 | 59 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
* | NC_002947_CJ‑RC | 2,821,395 | 0 | G | . | 36.8% | 38.7 / 22.6 | 19 | intergenic (‑64/‑327) | PP_2474/PP_2475 | glutathione S‑transferase family protein/TetR family transcriptional regulator |
* | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 36.7% | 76.3 / 13.1 | 49 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
* | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 34.5% | 55.6 / 15.1 | 63 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
* | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 32.2% | 95.6 / 13.6 | 59 | E610A (GAG→GCG) | betT‑I | choline transporter |
* | NC_002947_CJ‑RC | 441,318 | 0 | T | G | 30.4% | 67.6 / 10.2 | 47 | W67G (TGG→GGG) | bioF | 8‑amino‑7‑oxononanoate synthase |
* | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 30.4% | 29.7 / 18.8 | 23 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 29.2% | 28.4 / 16.1 | 24 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 29.2% | 26.0 / 16.1 | 24 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 5,743,289 | 0 | C | A | 29.2% | 38.1 / 17.8 | 24 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
* | NC_002947_CJ‑RC | 2,737,081 | 0 | C | A | 25.0% | 109.6 / 11.5 | 49 | Q1327K (CAA→AAA) | PP_2394 | leucine‑rich repeat‑containing protein |
* | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 24.6% | 105.8 / 11.9 | 58 | T140A (ACC→GCC) | PP_1551 | replication protein O |
Marginal new junction evidence (lowest skew 10 of 44 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947_CJ‑RC | = 652782 | 74 (0.940) | 19 (0.280) | 13/250 | 6.3 | 37.4% | 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 | 34 (0.430) | 16 (0.210) | 15/280 | 6.5 | 31.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947_CJ‑RC | 2957165 = | 36 (0.480) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 17 (0.220) +GCC |
15/284 | 6.6 | 94.5% | 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 | 4809877 = | 12 (0.150) | 10 (0.170) | 10/220 | 6.6 | 34.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991750 | 29 (0.490) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 17 (0.240) | 12/266 | 7.2 | 43.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | 5991580 = | 42 (0.580) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 14 (0.210) | 10/250 | 7.5 | 37.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991764 | 44 (0.650) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5684230 | 3 (0.040) | 12 (0.160) +CGGG |
10/282 | 8.5 | 80.5% | 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 | = 5991586 | 44 (0.560) | 10 (0.140) | 9/274 | 8.7 | 18.6% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | NC_002947_CJ‑RC | 5991778 = | 46 (0.620) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | 4809877 = | 12 (0.150) | 7 (0.110) | 6/238 | 9.2 | 26.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | 5991594 = | 30 (0.470) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 3968879 | NA (NA) | 6 (0.080) | 6/276 | 10.4 | 8.6% | coding (1007/1179 nt) | PP_3498 | transposase |
? | NC_002947_CJ‑RC | 3968942 = | 67 (0.860) | coding (1070/1179 nt) | PP_3498 | transposase |