mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,474,272 | 0 | C | T | 73.1% | 32.6 / 10.8 | 27 | R94H (CGT→CAT) | rpsL | 30S ribosomal subunit protein S12 |
| * | NC_000913 | 2,936,855 | 0 | T | G | 72.2% | 52.9 / 12.6 | 36 | A424A (GCT→GCG) | fucI | L‑fucose isomerase |
| * | NC_000913 | 3,474,424 | 0 | T | G | 71.4% | 40.1 / 11.8 | 28 | K43N (AAA→AAC) | rpsL | 30S ribosomal subunit protein S12 |
| * | NC_000913 | 4,037,496 | 0 | A | T | 71.4% | 24.3 / 14.1 | 29 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,729,440 | 0 | C | T | 65.4% | 23.1 / 18.9 | 26 | noncoding (106/160 nt) | xylZ | small RNA XylZ |
| * | NC_000913 | 3,729,441 | 0 | C | T | 64.0% | 20.6 / 18.7 | 26 | noncoding (105/160 nt) | xylZ | small RNA XylZ |
| * | NC_000913 | 2,765,411 | 1 | . | G | 33.3% | 0.1 / 11.0 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 2 | . | C | 33.3% | 0.2 / 11.0 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 3 | . | A | 33.3% | ‑0.3 / 10.7 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 4 | . | C | 33.3% | 0.3 / 10.9 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 5 | . | T | 33.3% | ‑0.0 / 10.6 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 6 | . | A | 33.3% | 0.1 / 10.3 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 7 | . | T | 33.3% | ‑0.6 / 11.2 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 2,765,411 | 8 | . | G | 33.3% | ‑0.1 / 11.2 | 9 | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| * | NC_000913 | 4,423,825 | 0 | C | T | 28.1% | 40.1 / 17.0 | 34 | P42P (CCC→CCT) | ulaF | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| * | NC_000913 | 3,472,337 | 0 | G | T | 25.6% | 53.1 / 17.3 | 39 | T393N (ACT→AAT) | fusA | elongation factor G |
| * | NC_000913 | 3,474,355 | 0 | G | C | 22.9% | 57.8 / 23.0 | 35 | Y66* (TAC→TAG) | rpsL | 30S ribosomal subunit protein S12 |
| * | NC_000913 | 4,000,594 | 0 | C | A | 21.7% | 86.0 / 16.8 | 46 | A155S (GCG→TCG) ‡ | yigE | DUF2233 domain‑containing protein YigE |
| * | NC_000913 | 581,337 | 0 | G | A | 20.7% | 49.6 / 10.7 | 29 | L168L (CTG→CTA) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 4,000,592 | 0 | C | A | 20.0% | 82.4 / 14.8 | 45 | A155A (GCG→GCT) ‡ | yigE | DUF2233 domain‑containing protein YigE |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 6 (0.240) | 6/484 | 1.9 | 18.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4215396 = | 26 (1.020) | intergenic (+187/‑82) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A | |||||
| * | ? | NC_000913 | 4436762 = | 25 (0.980) | 4 (0.160) | 4/486 | 2.4 | 13.8% | coding (8/741 nt) | cysQ | 3'(2'),5'‑bisphosphate nucleotidase |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2102943 | NA (NA) | 4 (0.160) | 4/486 | 2.4 | 16.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2115039 = | 20 (0.780) | coding (858/1395 nt) | wcaM | putative colanic acid biosynthesis protein WcaM | |||||
| * | ? | NC_000913 | = 1676530 | 36 (1.410) | 3 (0.120) | 3/478 | 2.7 | 8.5% | coding (1374/1533 nt) | pntA | pyridine nucleotide transhydrogenase subunit alpha |
| ? | NC_000913 | 1677140 = | 29 (1.150) | coding (764/1533 nt) | pntA | pyridine nucleotide transhydrogenase subunit alpha | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 3 (0.120) | 3/486 | 2.8 | 12.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2421265 = | 21 (0.820) | coding (645/648 nt) | yfcG | disulfide bond oxidoreductase YfcG | |||||
| * | ? | NC_000913 | 577820 = | 24 (0.940) | 3 (0.120) | 3/484 | 2.8 | 11.1% | coding (208/498 nt) | rrrD | lysozyme |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 3 (0.120) | 3/486 | 2.8 | 8.6% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1302240 | 32 (1.250) | coding (1059/1632 nt) | oppA | oligopeptide ABC transporter periplasmic binding protein | |||||