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 55 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 349,993 | 0 | T | G | 37.0% | 62.8 / 11.8 | 46 | V526G (GTT→GGT) | prpE | propionate‑‑CoA ligase |
| * | CP009273 | 595,032 | 0 | T | G | 32.3% | 93.9 / 16.9 | 62 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | CP009273 | 3,588,381 | 0 | C | A | 31.8% | 108.3 / 12.3 | 63 | A154S (GCG→TCG) | livM | leucine/isoleucine/valine transporter subunit |
| * | CP009273 | 3,199,794 | 0 | C | T | 30.7% | 160.2 / 42.9 | 101 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | CP009273 | 324,514 | 0 | T | G | 29.7% | 59.9 / 10.0 | 38 | T178P (ACC→CCC) | betI | choline‑inducible betIBA‑betT divergent operon transcriptional repressor |
| * | CP009273 | 1,010,972 | 0 | G | T | 28.6% | 156.9 / 18.3 | 77 | intergenic (+57/‑199) | pqiC/rmf | DUF330 family putative lipoprotein/ribosome modulation factor |
| * | CP009273 | 2,977,800 | 0 | A | C | 28.6% | 154.4 / 12.0 | 84 | G384G (GGT→GGG) | yqeF | short chain acyltransferase |
| * | CP009273 | 3,659,062 | 0 | C | A | 28.5% | 261.5 / 38.5 | 130 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | CP009273 | 324,520 | 0 | C | T | 28.2% | 68.5 / 10.5 | 39 | D176N (GAT→AAT) ‡ | betI | choline‑inducible betIBA‑betT divergent operon transcriptional repressor |
| * | CP009273 | 324,518 | 0 | A | T | 27.5% | 78.9 / 10.9 | 40 | D176E (GAT→GAA) ‡ | betI | choline‑inducible betIBA‑betT divergent operon transcriptional repressor |
| * | CP009273 | 1,009,475 | 0 | A | G | 27.4% | 142.4 / 12.2 | 73 | E254G (GAA→GGA) | pqiB | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| * | CP009273 | 4,594,161 | 0 | C | T | 27.2% | 213.0 / 49.2 | 126 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | CP009273 | 2,380,341 | 0 | G | A | 26.6% | 205.9 / 45.5 | 111 | intergenic (+31/‑72) | yfbL/yfbM | putative peptidase/DUF1877 family protein |
| * | CP009273 | 1,155,293 | 0 | A | G | 26.4% | 143.2 / 13.3 | 72 | I572T (ATC→ACC) | fhuE | ferric‑rhodotorulic acid outer membrane transporter |
| * | CP009273 | 2,372,447 | 0 | C | T | 26.3% | 74.8 / 16.7 | 58 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| * | CP009273 | 3,659,058 | 0 | T | C | 25.8% | 232.3 / 33.4 | 130 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | CP009273 | 2,819,821 | 0 | G | A | 25.6% | 149.6 / 23.2 | 78 | G24E (GGA→GAA) | srlE | glucitol/sorbitol‑specific enzyme IIB component of PTS |
| * | CP009273 | 630,548 | 0 | A | T | 25.6% | 175.2 / 21.5 | 82 | D95E (GAT→GAA) | ybdM | Spo0J family protein, ParB‑like nuclease domain |
| * | CP009273 | 1,483,431 | 0 | G | T | 25.5% | 253.6 / 19.5 | 106 | G315C (GGT→TGT) | aldA | aldehyde dehydrogenase A, NAD‑linked |
| * | CP009273 | 3,611,723 | 0 | G | A | 25.4% | 110.5 / 12.9 | 57 | K196K (AAG→AAA) | nikE | nickel transporter subunit |
| Marginal new junction evidence (lowest skew 10 of 56 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 4161745 | 16 (0.170) | 29 (0.020) +G |
17/232 | 3.4 | 29.0% | intergenic (+61/‑240) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 8 = | 127 (0.040) | intergenic (–/‑1091) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | 360104 = | 53 (0.550) | 15 (0.170) +AATTCC |
12/222 | 4.3 | 25.2% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | 4033989 = | 41 (0.430) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 4532499 = | 57 (0.600) | 14 (0.160) | 11/216 | 4.5 | 14.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 107 (1.210) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | 3416618 = | 43 (0.450) | 12 (0.140) +GAATTAATTCC |
9/212 | 5.0 | 24.0% | intergenic (+65/+164) | yhdZ/rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| ? | CP009273 | 4033989 = | 41 (0.430) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | = 4034057 | 28 (0.290) | 17 (0.010) +G |
10/232 | 5.1 | 18.1% | intergenic (+61/+209) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | KX077536 | 8 = | 127 (0.040) | intergenic (–/‑1091) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | 3416721 = | 36 (0.380) | 12 (0.010) +G |
8/232 | 5.7 | 12.9% | intergenic (+168/+61) | yhdZ/rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| ? | KX077536 | 8 = | 127 (0.040) | intergenic (–/‑1091) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | = 1203261 | 110 (1.150) | 6 (0.070) | 6/202 | 5.9 | 6.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 90 (1.090) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 4161761 | 15 (0.160) | 8 (0.000) +G |
7/232 | 6.1 | 3.0% | intergenic (+77/‑224) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 24 = | 501 (0.160) | intergenic (–/‑1075) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | 360196 = | 36 (0.380) | 8 (0.000) +G |
7/232 | 6.1 | 2.9% | intergenic (‑130/+465) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | KX077536 | 24 = | 501 (0.160) | intergenic (–/‑1075) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | 360104 = | 53 (0.550) | 6 (0.000) +AATTCCCC |
6/218 | 6.2 | 10.8% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | KX077536 | 8127 = | NA (NA) | intergenic (+52/–) | unknown/– | cat/– | |||||