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 234 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 792,056 | 0 | C | T | 53.8% | 13.2 / 28.9 | 27 | T16I (ACT→ATT) | modC | molybdenum ABC transporter ATP‑binding protein ModC |
| * | NZ_CP009273 | 595,035 | 0 | T | G | 51.5% | 9.8 / 26.6 | 33 | V289G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 108,789 | 0 | T | C | 51.3% | 25.2 / 41.4 | 37 | S100G (AGC→GGC) | zapD | cell division protein ZapD |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 50.0% | 3.4 / 18.0 | 33 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 2,371,314 | 0 | G | A | 48.6% | 25.2 / 19.7 | 38 | F475F (TTC→TTT) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase |
| * | NZ_CP009273 | 832,042 | 0 | C | G | 47.6% | 33.3 / 15.7 | 42 | A79G (GCG→GGG) | hcxB | hydroxycarboxylate dehydrogenase HcXB |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 46.9% | 25.5 / 41.0 | 49 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 2,290,243 | 0 | T | G | 46.8% | 30.4 / 12.4 | 47 | L87F (TTA→TTC) | ccmB | heme exporter protein CcmB |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 45.5% | 30.3 / 28.5 | 55 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 3,254,414 | 0 | A | C | 45.3% | 21.8 / 27.4 | 53 | V455G (GTG→GGG) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase |
| * | NZ_CP009273 | 4,058,958 | 0 | G | A | 44.6% | 61.2 / 29.1 | 56 | L57L (CTG→TTG) | yihO | MFS transporter |
| * | NZ_CP009273 | 700,996 | 0 | C | A | 43.2% | 61.2 / 12.9 | 45 | P533T (CCG→ACG) | nagE | PTS N‑acetyl glucosamine transporter subunit IIABC |
| * | NZ_CP009273 | 3,199,811 | 0 | C | A | 42.6% | 86.9 / 29.5 | 54 | intergenic (‑196/‑11) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 70,068 | 0 | A | C | 42.5% | 28.5 / 13.5 | 40 | V314G (GTA→GGA) | thiP | thiamine/thiamine pyrophosphate ABC transporter permease ThiP |
| * | NZ_CP009273 | 1,819,318 | 0 | G | A | 42.3% | 26.2 / 12.7 | 26 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy |
| * | NZ_CP009273 | 4,612,067 | 0 | A | G | 42.2% | 128.8 / 48.6 | 116 | E161G (GAG→GGG) | yjjJ | type II toxin‑antitoxin system HipA family toxin YjjJ |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 42.1% | 121.5 / 68.5 | 107 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 4,213,521 | 0 | T | G | 41.8% | 50.5 / 11.8 | 55 | K12N (AAA→AAC) | iclR | glyoxylate bypass operon transcriptional repressor IclR |
| * | NZ_CP009273 | 2,134,407 | 0 | A | C | 41.3% | 55.9 / 16.8 | 63 | G229G (GGT→GGG) | asmA | outer membrane assembly protein AsmA |
| * | NZ_CP009273 | 687,303 | 0 | A | G | 41.0% | 89.2 / 28.7 | 79 | intergenic (‑63/+27) | corC/ybeY | CNNM family magnesium/cobalt transport protein CorC/rRNA maturation RNase YbeY |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 376748 = | NA (NA) | 4 (0.060) | 4/142 | 4.3 | NA | intergenic (‑5/‑59) | BW25113_RS01855/BW25113_RS01870 | transferase/IS3‑like element IS2 family transposase |
| ? | NZ_CP009273 | 376768 = | NA (NA) | intergenic (‑25/‑39) | BW25113_RS01855/BW25113_RS01870 | transferase/IS3‑like element IS2 family transposase | |||||
| * | ? | NZ_CP009273 | = 4031961 | NA (NA) | 7 (0.090) | 4/152 | 4.5 | 88.1% | noncoding (1083/2905 nt) | BW25113_RS19995 | 23S ribosomal RNA |
| ? | NZ_CP009273 | 4031966 = | 1 (0.010) | noncoding (1088/2905 nt) | BW25113_RS19995 | 23S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 1865520 | 54 (0.690) | 3 (0.050) | 3/132 | 4.5 | 6.8% | coding (879/1476 nt) | cdgI | GGDEF domain‑containing protein |
| ? | NZ_CP009273 | = 1865506 | 38 (0.590) | coding (865/1476 nt) | cdgI | GGDEF domain‑containing protein | |||||
| * | ? | NZ_CP009273 | = 223332 | NA (NA) | 7 (0.090) | 4/152 | 4.5 | NA | noncoding (1087/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA |
| ? | NZ_CP009273 | 223337 = | NA (NA) | noncoding (1092/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 4223326 | 107 (1.370) | 4 (0.050) | 4/158 | 4.6 | 3.7% | intergenic (‑165/‑360) | lysC/pgi | lysine‑sensitive aspartokinase 3/glucose‑6‑phosphate isomerase |
| ? | NZ_CP009273 | 4223330 = | 104 (1.350) | intergenic (‑169/‑356) | lysC/pgi | lysine‑sensitive aspartokinase 3/glucose‑6‑phosphate isomerase | |||||
| * | ? | NZ_CP009273 | = 3707970 | 83 (1.060) | 4 (0.060) | 3/142 | 4.7 | 5.1% | coding (1785/2334 nt) | bisC | biotin sulfoxide reductase |
| ? | NZ_CP009273 | = 3707984 | 75 (1.080) | coding (1771/2334 nt) | bisC | biotin sulfoxide reductase | |||||
| * | ? | NZ_CP009273 | 2823578 = | 60 (0.770) | 4 (0.060) | 3/140 | 4.7 | 6.9% | coding (407/966 nt) | gutQ | arabinose‑5‑phosphate isomerase GutQ |
| ? | NZ_CP009273 | 2823644 = | 56 (0.820) | coding (473/966 nt) | gutQ | arabinose‑5‑phosphate isomerase GutQ | |||||
| * | ? | NZ_CP009273 | = 2640641 | 47 (0.600) | 3 (0.040) | 3/140 | 4.7 | 6.7% | coding (44/2313 nt) | pbpC | peptidoglycan glycosyltransferase PbpC |
| ? | NZ_CP009273 | = 2640710 | 43 (0.630) | coding (4937/4962 nt) | yfhM | alpha2‑macroglobulin | |||||
| * | ? | NZ_CP009273 | 82062 = | 105 (1.340) | 3 (0.040) | 3/142 | 4.7 | 3.1% | intergenic (‑64/‑55) | BW25113_RS25405/ilvI | protein YabR/acetolactate synthase 3 large subunit |
| ? | NZ_CP009273 | 82155 = | 92 (1.330) | coding (39/1725 nt) | ilvI | acetolactate synthase 3 large subunit | |||||
| * | ? | NZ_CP009273 | = 299793 | 83 (1.060) | 3 (0.040) | 3/146 | 4.8 | 4.0% | coding (101/330 nt) | ykgJ | YkgJ family cysteine cluster protein |
| ? | NZ_CP009273 | = 299801 | 69 (0.970) | coding (93/330 nt) | ykgJ | YkgJ family cysteine cluster protein | |||||