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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,040,623 | 0 | G | A | 78.8% | 127.9 / 43.9 | 85 | noncoding (107/120 nt) | rrfA | 5S ribosomal RNA |
| * | NC_000913 | 4,166,856 | 0 | G | A | 51.2% | 14.3 / 59.8 | 41 | noncoding (198/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 1,001,094 | 0 | G | T | 36.6% | 118.7 / 22.4 | 93 | E627* (GAG→TAG) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 2,990,480 | 0 | C | A | 35.7% | 163.2 / 27.3 | 126 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,911,533 | 0 | C | A | 33.3% | 179.8 / 23.0 | 129 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 58,065 | 0 | C | A | 32.6% | 138.7 / 16.7 | 92 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 4,074,572 | 0 | C | A | 31.6% | 117.2 / 16.0 | 81 | P278P (CCC→CCA) | yihV | 6‑deoxy‑6‑sulfofructose kinase |
| * | NC_000913 | 12,152 | 0 | G | T | 31.4% | 191.7 / 13.0 | 124 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 3,791,179 | 0 | G | T | 29.7% | 175.6 / 11.2 | 101 | P56Q (CCG→CAG) | tdh | threonine dehydrogenase |
| * | NC_000913 | 847,955 | 0 | G | A | 29.5% | 204.2 / 45.9 | 129 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,466,438 | 0 | T | G | 28.9% | 54.7 / 22.7 | 47 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,466,633 | 0 | C | A | 28.4% | 176.9 / 14.5 | 102 | P30H (CCT→CAT) | intS | prophage CPS‑53 integrase |
| * | NC_000913 | 2,722,838 | 0 | G | T | 28.3% | 222.1 / 13.1 | 113 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 2,365,840 | 0 | T | G | 27.8% | 176.0 / 10.8 | 109 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 442,025 | 0 | C | A | 27.6% | 151.3 / 13.0 | 87 | L159L (CTC→CTA) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 1,286,870 | 0 | C | A | 27.6% | 97.5 / 29.1 | 58 | S54S (TCC→TCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 4,360,965 | 0 | C | A | 27.6% | 320.5 / 20.9 | 156 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 141,849 | 0 | C | A | 27.1% | 234.4 / 10.2 | 108 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 1,502,770 | 0 | T | C | 27.0% | 102.4 / 15.1 | 74 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 3,741,871 | 0 | G | T | 26.5% | 222.6 / 17.0 | 117 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1411899 = | 110 (1.200) | 15 (0.180) | 12/536 | 4.1 | 12.0% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 119 (1.430) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 781222 | 58 (0.630) | 7 (0.100) | 7/436 | 4.7 | 13.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 47 (0.690) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 696741 | 55 (0.600) | 10 (0.150) | 7/432 | 4.7 | 19.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 44 (0.660) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 696469 | 79 (0.860) | 10 (0.110) +TAGAAT |
8/576 | 5.6 | 13.1% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696802 = | 57 (0.620) | noncoding (29/75 nt) | glnW | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 4606166 | 91 (1.000) | 4 (0.060) | 4/410 | 5.8 | 6.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 57 (0.890) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 696506 | 81 (0.890) | 6 (0.080) +45 bp |
5/498 | 6.2 | 8.8% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 65 (0.710) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | = 805862 | 72 (0.790) | 6 (0.070) | 6/574 | 6.4 | 8.1% | intergenic (+98/+136) | ybhJ/ybhC | putative hydratase YbhJ/outer membrane lipoprotein YbhC |
| ? | NC_000913 | 805955 = | 65 (0.730) | intergenic (+191/+43) | ybhJ/ybhC | putative hydratase YbhJ/outer membrane lipoprotein YbhC | |||||
| * | ? | NC_000913 | = 2653502 | 96 (1.050) | 4 (0.050) | 4/520 | 6.9 | 4.3% | intergenic (‑47/‑353) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653825 = | 92 (1.140) | intergenic (‑370/‑30) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2357713 | 85 (0.930) | 6 (0.070) +C |
5/586 | 6.9 | 6.1% | coding (810/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357910 = | 99 (1.080) | intergenic (+107/+132) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3469040 | 106 (1.160) | 4 (0.050) | 4/548 | 7.1 | 3.9% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 101 (1.190) | coding (510/2694 nt) | chiA | endochitinase | |||||