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 (highest frequency 20 of 39 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,503,229 | 0 | G | A | 52.6% | 10.8 / 236.5 | 152 | P68L (CCT→CTT) | insG | IS4 family putative transposase |
| * | NC_000913 | 4,037,496 | 0 | A | T | 48.0% | 71.8 / 309.1 | 154 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,054,888 | 0 | A | C | 36.5% | 167.3 / 11.3 | 98 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.0% | 162.6 / 31.4 | 97 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.0% | 133.8 / 29.7 | 97 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,886 | 0 | G | T | 33.0% | 150.7 / 36.9 | 98 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,445 | 0 | C | A | 32.5% | 228.5 / 22.0 | 114 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.2% | 162.8 / 17.3 | 112 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,365,840 | 0 | T | G | 30.2% | 264.1 / 13.1 | 170 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 3,741,871 | 0 | G | T | 29.9% | 216.4 / 14.8 | 117 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 442,025 | 0 | C | A | 28.0% | 189.9 / 10.7 | 107 | L159L (CTC→CTA) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 2,159,413 | 0 | C | T | 27.9% | 134.7 / 15.7 | 69 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 1,922,815 | 0 | C | A | 27.7% | 188.9 / 22.2 | 112 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 1,001,094 | 0 | G | T | 27.4% | 197.5 / 13.1 | 113 | E627* (GAG→TAG) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 4,427,822 | 0 | C | A | 27.4% | 263.6 / 20.3 | 146 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 847,955 | 0 | G | A | 26.7% | 233.3 / 52.4 | 147 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,159,415 | 0 | C | G | 25.9% | 151.8 / 16.2 | 69 | L344V (CTG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 799,484 | 0 | C | A | 25.7% | 227.6 / 14.3 | 109 | S300* (TCG→TAG) | pgl | 6‑phosphogluconolactonase |
| * | NC_000913 | 2,288,418 | 0 | G | T | 25.4% | 289.6 / 18.1 | 142 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 1,466,438 | 0 | T | G | 25.0% | 91.6 / 28.5 | 53 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1411899 = | 131 (1.200) | 23 (0.230) | 19/546 | 4.5 | 14.5% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 151 (1.510) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 4606166 | 110 (1.000) | 12 (0.160) | 12/420 | 4.9 | 14.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 63 (0.820) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1287329 | 70 (0.640) | 7 (0.090) | 6/424 | 7.4 | 12.3% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 50 (0.640) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 2357730 | 123 (1.120) | 7 (0.070) | 7/518 | 8.1 | 5.9% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 115 (1.210) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 781222 | 58 (0.530) | 6 (0.070) | 5/446 | 8.2 | 10.9% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 55 (0.670) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2817942 | 68 (0.620) | 6 (0.060) | 6/558 | 9.1 | 7.7% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 80 (0.780) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 696741 | 84 (0.770) | 5 (0.060) | 3/442 | 9.4 | 7.6% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 60 (0.740) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1286728 | 99 (0.900) | 4 (0.040) | 4/556 | 10.2 | 4.7% | coding (20/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287263 = | 69 (0.680) | noncoding (66/85 nt) | tyrV | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 819180 | 109 (1.000) | 4 (0.040) | 4/586 | 10.6 | 3.8% | coding (133/246 nt) | moaD | molybdopterin synthase sulfur carrier subunit |
| ? | NC_000913 | 819524 = | 96 (0.890) | coding (230/453 nt) | moaE | molybdopterin synthase catalytic subunit | |||||
| * | ? | NC_000913 | = 781544 | 70 (0.640) | 4 (0.040) | 4/594 | 10.7 | 4.8% | intergenic (+100/‑33) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 89 (0.820) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||