mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
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 | 4,190,035 | 0 | C | G | 74.4% | 251.7 / 94.7 | 129 | R84G (CGT→GGT) | yjaZ | stationary phase growth adaptation protein |
| * | NC_000913 | 909,400 | 0 | C | A | 71.2% | 96.7 / 50.0 | 66 | M550I (ATG→ATT) | poxB | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| * | NC_000913 | 753,658 | 0 | C | A | 68.5% | 80.0 / 68.5 | 74 | A271S (GCG→TCG) | gltA | citrate synthase |
| * | NC_000913 | 4,188,572 | 0 | C | T | 49.5% | 5.6 / 133.4 | 96 | R1075C (CGT→TGT) ‡ | rpoC | RNA polymerase, beta prime subunit |
| * | NC_000913 | 4,296,060 | 0 | C | T | 45.0% | 61.2 / 141.0 | 109 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,188,573 | 0 | G | T | 44.8% | 42.7 / 126.0 | 96 | R1075L (CGT→CTT) ‡ | rpoC | RNA polymerase, beta prime subunit |
| * | NC_000913 | 1,196,220 | 0 | C | T | 37.1% | 67.5 / 60.3 | 62 | H366H (CAC→CAT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,232 | 0 | C | T | 31.8% | 88.7 / 50.5 | 64 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,245 | 0 | T | C | 27.1% | 102.6 / 37.6 | 59 | L375L (TTA→CTA) ‡ | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,247 | 0 | A | G | 27.1% | 104.7 / 38.8 | 59 | L375L (TTA→TTG) ‡ | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 909,353 | 0 | G | A | 23.9% | 122.0 / 36.3 | 67 | A566V (GCG→GTG) | poxB | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| * | NC_000913 | 380,013 | 0 | G | . | 23.1% | 65.2 / 17.2 | 27 | intergenic (‑132/+56) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 104 (1.120) | 25 (0.290) | 23/260 | 3.0 | 17.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 132 (1.520) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 2375828 = | 33 (0.370) | 26 (0.290) | 23/270 | 3.1 | 44.1% | coding (135/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515617 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 608010 = | NA (NA) | 23 (0.250) | 20/278 | 3.7 | 34.8% | noncoding (4/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 729667 | 43 (0.460) | coding (85/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 4542690 | 95 (1.020) | 11 (0.130) | 10/260 | 5.6 | 9.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 130 (1.500) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.310) | 9 (0.110) | 9/246 | 5.6 | 25.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3811200 = | 89 (0.960) | 9 (0.110) | 9/254 | 5.8 | 9.3% | intergenic (‑48/+50) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| ? | NC_000913 | 3811236 = | 95 (1.120) | intergenic (‑84/+14) | mutM/rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 | |||||
| * | ? | NC_000913 | 4426579 = | 101 (1.090) | 4 (0.050) | 4/252 | 7.7 | 4.2% | intergenic (+22/+49) | rplI/yjfZ | 50S ribosomal subunit protein L9/uncharacterized protein |
| ? | NC_000913 | 4426606 = | 91 (1.080) | intergenic (+49/+22) | rplI/yjfZ | 50S ribosomal subunit protein L9/uncharacterized protein | |||||
| * | ? | NC_000913 | = 4219847 | 112 (1.210) | 4 (0.050) | 4/254 | 7.7 | 3.8% | coding (1252/1737 nt) | aceK | isocitrate dehydrogenase kinase/phosphatase |
| ? | NC_000913 | = 4219854 | 99 (1.170) | coding (1259/1737 nt) | aceK | isocitrate dehydrogenase kinase/phosphatase | |||||
| * | ? | NC_000913 | = 3986614 | 106 (1.140) | 4 (0.050) | 4/256 | 7.7 | 3.9% | noncoding (183/207 nt) | glmZ | sRNA antisense activator of glmS mRNA, Hfq‑dependent |
| ? | NC_000913 | = 3986622 | 99 (1.160) | noncoding (191/207 nt) | glmZ | sRNA antisense activator of glmS mRNA, Hfq‑dependent | |||||
| * | ? | NC_000913 | = 523710 | 76 (0.820) | 5 (0.060) | 4/262 | 7.8 | 6.4% | coding (450/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 523728 | 74 (0.850) | coding (468/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||