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 569 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 54.5% | 46.6 / 194.6 | 145 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 1,350,458 | 0 | T | G | 52.8% | 45.9 / 70.5 | 53 | T304P (ACC→CCC) | sapA | peptide ABC transporter substrate‑binding protein SapA |
| * | NZ_CP009273 | 4,594,167 | 0 | C | T | 52.1% | 84.0 / 210.6 | 145 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 51.8% | 36.5 / 119.4 | 85 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 766,353 | 0 | T | G | 51.6% | 85.7 / 125.0 | 95 | intergenic (+286/‑561) | mngB/cydA | mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I |
| * | NZ_CP009273 | 1,125,835 | 0 | A | C | 50.7% | 75.1 / 86.9 | 69 | V162G (GTA→GGA) | flgA | flagellar basal body P‑ring formation chaperone FlgA |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 49.5% | 61.0 / 95.7 | 95 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 2,290,243 | 0 | T | G | 49.4% | 97.4 / 21.6 | 86 | L87F (TTA→TTC) | ccmB | heme exporter protein CcmB |
| * | NZ_CP009273 | 3,126,661 | 0 | T | G | 49.3% | 56.4 / 38.7 | 71 | H219P (CAC→CCC) | yghS | dTMP kinase |
| * | NZ_CP009273 | 2,380,362 | 0 | C | T | 48.8% | 63.2 / 79.1 | 86 | intergenic (+52/‑51) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 2,380,357 | 0 | A | T | 48.0% | 76.9 / 47.8 | 77 | intergenic (+47/‑56) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 883,470 | 0 | T | G | 47.0% | 113.3 / 23.5 | 100 | intergenic (+55/+120) | rcdA/ybjL | DNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter |
| * | NZ_CP009273 | 822,955 | 0 | T | G | 46.9% | 75.7 / 14.2 | 65 | T495P (ACC→CCC) | ybhF | ATP‑binding cassette domain‑containing protein |
| * | NZ_CP009273 | 353,601 | 0 | C | A | 46.7% | 57.9 / 41.5 | 60 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| * | NZ_CP009273 | 2,852,466 | 0 | T | G | 46.5% | 34.6 / 31.6 | 72 | V672G (GTG→GGG) | mutS | DNA mismatch repair protein MutS |
| * | NZ_CP009273 | 642,666 | 0 | A | C | 46.3% | 68.9 / 20.1 | 67 | G100G (GGT→GGG) | citG | triphosphoribosyl‑dephospho‑CoA synthase CitG |
| * | NZ_CP009273 | 2,669,465 | 0 | C | A | 46.0% | 69.9 / 29.4 | 50 | L240F (TTG→TTT) | yphD | ABC transporter permease |
| * | NZ_CP009273 | 3,734,269 | 0 | T | G | 45.0% | 184.2 / 59.4 | 160 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate transaminase |
| * | NZ_CP009273 | 2,371,314 | 0 | G | A | 44.6% | 40.1 / 32.3 | 56 | F475F (TTC→TTT) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase |
| * | NZ_CP009273 | 2,367,400 | 0 | A | C | 44.6% | 104.4 / 14.9 | 92 | G361G (GGT→GGG) | menE | o‑succinylbenzoate‑‑CoA ligase |
| Marginal new junction evidence (lowest skew 10 of 177 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | = 729706 | NA (NA) | 12 (0.110) | 10/154 | 3.5 | NA | pseudogene (103/1506 nt) | BW25113_RS03635 | RHS repeat protein |
| ? | NZ_CP009273 | = 729729 | NA (NA) | pseudogene (126/1506 nt) | BW25113_RS03635 | RHS repeat protein | |||||
| * | ? | NZ_CP009273 | = 727835 | 57 (0.480) | 12 (0.110) | 10/154 | 3.5 | 18.9% | coding (2797/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NZ_CP009273 | = 729729 | NA (NA) | pseudogene (126/1506 nt) | BW25113_RS03635 | RHS repeat protein | |||||
| * | ? | NZ_CP009273 | 3541266 = | 157 (1.330) | 9 (0.090) | 8/142 | 3.8 | 6.8% | intergenic (+32/+79) | gntT/malQ | gluconate transporter/4‑alpha‑glucanotransferase |
| ? | NZ_CP009273 | 3541310 = | 114 (1.160) | intergenic (+76/+35) | gntT/malQ | gluconate transporter/4‑alpha‑glucanotransferase | |||||
| * | ? | NZ_CP009273 | 727836 = | NA (NA) | 9 (0.080) | 9/154 | 3.8 | 16.3% | coding (2798/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NZ_CP009273 | 727859 = | 51 (0.430) | coding (2821/4194 nt) | rhsC | rhs element protein RhsC | |||||
| * | ? | NZ_CP009273 | = 322269 | 258 (2.190) | 8 (0.080) | 8/150 | 3.9 | 3.8% | coding (690/1671 nt) | betA | choline dehydrogenase |
| ? | NZ_CP009273 | = 322352 | 177 (1.700) | coding (607/1671 nt) | betA | choline dehydrogenase | |||||
| * | ? | NZ_CP009273 | 3615349 = | NA (NA) | 8 (0.070) | 8/154 | 4.0 | 100% | coding (2798/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NZ_CP009273 | 3615372 = | 0 (0.000) | coding (2821/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NZ_CP009273 | 281585 = | 127 (1.080) | 8 (0.070) | 8/154 | 4.0 | 6.4% | coding (480/1383 nt) | yagG | MFS transporter |
| ? | NZ_CP009273 | 281607 = | 119 (1.110) | coding (502/1383 nt) | yagG | MFS transporter | |||||
| * | ? | NZ_CP009273 | 278994 = | 123 (1.040) | 8 (0.070) | 8/154 | 4.0 | 6.6% | coding (83/1968 nt) | yagF | xylonate dehydratase YagF |
| ? | NZ_CP009273 | 279036 = | 115 (1.080) | coding (125/1968 nt) | yagF | xylonate dehydratase YagF | |||||
| * | ? | NZ_CP009273 | = 278223 | 179 (1.520) | 11 (0.100) | 8/154 | 4.0 | 5.9% | coding (235/909 nt) | yagE | 2‑keto‑3‑deoxygluconate aldolase |
| ? | NZ_CP009273 | = 278229 | 191 (1.790) | coding (241/909 nt) | yagE | 2‑keto‑3‑deoxygluconate aldolase | |||||
| * | ? | NZ_CP009273 | = 299793 | 278 (2.350) | 9 (0.080) | 8/156 | 4.1 | 3.3% | coding (101/330 nt) | ykgJ | YkgJ family cysteine cluster protein |
| ? | NZ_CP009273 | = 299801 | 274 (2.530) | coding (93/330 nt) | ykgJ | YkgJ family cysteine cluster protein | |||||