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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,911,533 | 0 | C | A | 39.8% | 124.2 / 21.3 | 108 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,779,583 | 0 | G | T | 35.4% | 143.1 / 15.2 | 99 | intergenic (‑282/‑34) | ydiP/ydiQ | putative DNA‑binding transcriptional regulator YdiP/putative electron transfer flavoprotein subunit YdiQ |
| * | NC_000913 | 1,351,463 | 0 | C | A | 33.3% | 95.4 / 10.0 | 66 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 442,471 | 0 | C | A | 32.6% | 138.8 / 10.6 | 89 | S308Y (TCC→TAC) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 32.4% | 223.7 / 14.8 | 111 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 4,540,411 | 0 | C | A | 31.4% | 183.0 / 10.8 | 118 | intergenic (‑910/‑546) | nanC/fimB | N‑acetylneuraminate outer membrane channel/Type 1 fimbriae regulatory protein FimB |
| * | NC_000913 | 834,674 | 0 | C | A | 29.9% | 132.5 / 11.2 | 77 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 4,261,040 | 0 | C | A | 28.3% | 250.5 / 11.5 | 120 | Q148K (CAA→AAA) | yjbM | DUF2713 domain‑containing protein YjbM |
| * | NC_000913 | 3,054,894 | 0 | G | T | 28.2% | 102.2 / 13.6 | 71 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,326,713 | 0 | C | A | 27.1% | 101.3 / 10.1 | 59 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,812,509 | 0 | G | T | 26.2% | 216.8 / 20.4 | 107 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 1,334,966 | 0 | A | C | 26.1% | 195.7 / 21.9 | 119 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,722,230 | 0 | G | T | 25.9% | 226.3 / 14.4 | 116 | intergenic (+181/+98) | insK/glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta |
| * | NC_000913 | 847,955 | 0 | G | A | 25.2% | 173.0 / 24.4 | 100 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,296,268 | 0 | T | C | 25.0% | 34.5 / 11.6 | 24 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,623,537 | 0 | G | A | 24.8% | 184.2 / 12.5 | 102 | G47S (GGT→AGT) | yhhH | PF15631 family protein YhhH |
| * | NC_000913 | 3,741,871 | 0 | G | T | 24.7% | 173.4 / 10.9 | 93 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,466,604 | 0 | G | A | 24.4% | 73.6 / 10.3 | 45 | pseudogene (1213/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 3,054,886 | 0 | G | T | 24.4% | 138.5 / 10.1 | 78 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,901,209 | 0 | C | T | 23.9% | 94.7 / 10.8 | 46 | W126* (TGG→TAG) | yoaE | TerC family inner membrane protein YoaE |
| 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 | = 4606166 | 70 (0.970) | 8 (0.160) | 7/410 | 3.7 | 14.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 43 (0.860) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2653419 | 73 (1.010) | 9 (0.140) | 9/538 | 4.2 | 12.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 58 (0.880) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2818275 | 40 (0.560) | 6 (0.110) | 5/430 | 4.7 | 14.8% | intergenic (‑1/+198) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818551 = | 40 (0.760) | intergenic (‑2/+2) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 3469004 | 81 (1.120) | 8 (0.110) | 8/576 | 4.8 | 9.3% | coding (850/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469308 = | 77 (1.090) | coding (546/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 1286906 | 34 (0.470) | 7 (0.100) | 7/548 | 4.9 | 19.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 26 (0.390) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781322 | 56 (0.780) | 6 (0.100) | 6/510 | 5.0 | 10.4% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 55 (0.880) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2357690 | 95 (1.320) | 6 (0.090) | 6/538 | 5.2 | 6.9% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 75 (1.140) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 781222 | 62 (0.860) | 6 (0.090) | 5/552 | 5.8 | 8.9% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781809 = | 65 (0.960) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 627525 | 83 (1.150) | 5 (0.070) | 5/570 | 5.9 | 6.2% | coding (1456/1611 nt) | entE | 2,3‑dihydroxybenzoate‑AMP ligase |
| ? | NC_000913 | 627887 = | 72 (1.030) | coding (194/858 nt) | entB | enterobactin synthase component B | |||||
| * | ? | NC_000913 | = 1287084 | 33 (0.460) | 7 (0.100) | 4/548 | 6.2 | 19.8% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 26 (0.390) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||