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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,027,233 | 0 | T | A | 34.5% | 62.2 / 20.9 | 55 | intergenic (+5/+376) | fre/fadA | NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 4,016,051 | 0 | T | C | 33.3% | 109.8 / 15.4 | 66 | D40G (GAT→GGT) | ysgA | putative dienelactone hydrolase |
| * | NC_000913 | 4,256,069 | 0 | G | C | 33.3% | 63.0 / 10.9 | 39 | P133R (CCG→CGG) | plsB | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| * | NC_000913 | 811,721 | 0 | T | G | 32.9% | 100.0 / 10.6 | 74 | V67G (GTG→GGG) | bioC | malonyl‑acyl carrier protein methyltransferase |
| * | NC_000913 | 288,382 | 0 | A | C | 31.8% | 81.7 / 10.6 | 65 | T532P (ACC→CCC) | yagH | putative xylosidase/arabinosidase |
| * | NC_000913 | 2,745,089 | 0 | A | C | 30.9% | 127.6 / 17.7 | 85 | V84G (GTG→GGG) | trmD | tRNA m(1)G37 methyltransferase |
| * | NC_000913 | 4,256,061 | 0 | C | T | 30.8% | 53.7 / 10.0 | 39 | E136K (GAA→AAA) | plsB | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| * | NC_000913 | 2,608,244 | 0 | T | G | 30.2% | 50.0 / 11.8 | 54 | V443G (GTG→GGG) | hyfF | hydrogenase 4 component F |
| * | NC_000913 | 2,291,598 | 0 | A | G | 29.8% | 118.1 / 13.0 | 67 | D271D (GAT→GAC) | ccmH | holocytochrome c synthase CcmH component |
| * | NC_000913 | 4,257,698 | 0 | T | G | 29.2% | 159.0 / 11.1 | 90 | V195G (GTT→GGT) | lexA | DNA‑binding transcriptional repressor LexA |
| * | NC_000913 | 4,451,570 | 0 | A | C | 29.1% | 151.7 / 15.5 | 87 | E171D (GAA→GAC) | ytfR | galactofuranose ABC transporter putative ATP binding subunit |
| * | NC_000913 | 728,024 | 0 | T | A | 28.6% | 73.9 / 10.2 | 42 | N237Y (AAT→TAT) | kdpA | K(+) transporting P‑type ATPase subunit KdpA |
| * | NC_000913 | 4,429,984 | 0 | T | G | 28.2% | 135.2 / 10.4 | 78 | L41V (TTG→GTG) | cycA | D‑serine/alanine/glycine/:H(+)symporter |
| * | NC_000913 | 37,338 | 0 | T | G | 28.0% | 172.8 / 15.0 | 97 | T163P (ACC→CCC) | caiC | carnitine‑‑CoA ligase |
| * | NC_000913 | 599,576 | 0 | T | G | 27.7% | 68.6 / 10.3 | 47 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 2,874,401 | 0 | T | C | 27.3% | 182.9 / 13.1 | 101 | D340G (GAT→GGT) | cysN | sulfate adenylyltransferase subunit 1 |
| * | NC_000913 | 651,267 | 0 | A | T | 26.8% | 132.5 / 16.7 | 71 | L197* (TTA→TAA) | citC | citrate lyase synthetase |
| * | NC_000913 | 651,297 | 0 | A | G | 26.4% | 148.9 / 11.1 | 72 | F187S (TTC→TCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 26.4% | 202.6 / 12.3 | 112 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 2,878,947 | 0 | C | T | 25.6% | 72.8 / 10.1 | 44 | E276K (GAA→AAA) | cas1 | multifunctional nuclease Cas1 |
| 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 | = 2565882 | 102 (1.370) | 4 (0.060) | 4/474 | 3.8 | 4.1% | coding (1003/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA |
| ? | NC_000913 | 2566036 = | 86 (1.190) | coding (849/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | = 1848743 | 44 (0.590) | 4 (0.050) | 4/488 | 3.8 | 8.8% | intergenic (‑67/‑94) | ydjA/sppA | putative oxidoreductase YdjA/protease IV, a signal peptide peptidase |
| ? | NC_000913 | 4168065 = | 39 (0.520) | noncoding (1407/1542 nt) | rrsB | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 3299583 = | 92 (1.240) | 3 (0.040) | 3/488 | 4.1 | 2.6% | coding (333/444 nt) | yhbP | putative FMN binding protein YhbP |
| ? | NC_000913 | 4271804 = | 133 (1.790) | coding (2068/2823 nt) | uvrA | UvrABC excision nuclease subunit A | |||||
| * | ? | NC_000913 | = 2841224 | 66 (0.890) | 3 (0.040) | 3/488 | 4.1 | 3.0% | coding (235/1425 nt) | ascB | 6‑phospho‑beta‑glucosidase AscB |
| ? | NC_000913 | 3907571 = | 126 (1.690) | coding (8/726 nt) | phoU | negative regulator of the pho regulon | |||||
| * | ? | NC_000913 | 2444089 = | 78 (1.050) | 3 (0.040) | 3/486 | 4.1 | 3.6% | coding (81/279 nt) | yfcL | PF08891 family protein YfcL |
| ? | NC_000913 | 3842931 = | 82 (1.110) | coding (859/1335 nt) | adeQ | adenine transporter | |||||
| * | ? | NC_000913 | = 2255147 | 40 (0.540) | 3 (0.040) +G |
3/486 | 4.1 | 3.3% | coding (40/942 nt) | rihB | pyrimidine‑specific ribonucleoside hydrolase RihB |
| ? | NC_000913 | = 3724072 | 137 (1.840) | coding (326/2070 nt) | glyS | glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_000913 | = 1848743 | 44 (0.590) | 3 (0.040) | 3/488 | 4.1 | 7.9% | intergenic (‑67/‑94) | ydjA/sppA | putative oxidoreductase YdjA/protease IV, a signal peptide peptidase |
| ? | NC_000913 | 4209553 = | 26 (0.350) | noncoding (1407/1542 nt) | rrsE | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 823463 | 79 (1.060) | 3 (0.040) | 3/488 | 4.1 | 3.6% | coding (277/1242 nt) | clsB | cardiolipin synthase B |
| ? | NC_000913 | 2909384 = | 83 (1.110) | coding (283/1638 nt) | pyrG | CTP synthetase | |||||