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 29 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 847,955 | 0 | G | A | 35.4% | 103.2 / 43.4 | 96 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,990,480 | 0 | C | A | 32.3% | 205.8 / 10.3 | 127 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 2,288,418 | 0 | G | T | 31.4% | 230.3 / 25.6 | 137 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 1,922,815 | 0 | C | A | 31.0% | 153.5 / 19.2 | 100 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.6% | 197.5 / 13.7 | 121 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,326,713 | 0 | C | A | 30.5% | 189.6 / 11.4 | 105 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,812,509 | 0 | G | T | 29.7% | 254.0 / 17.0 | 128 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 2,818,324 | 0 | G | A | 29.2% | 92.6 / 46.6 | 65 | intergenic (‑50/+149) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| * | NC_000913 | 782,194 | 0 | T | G | 29.0% | 90.8 / 10.4 | 62 | L37R (CTA→CGA) | nadA | quinolinate synthase |
| * | NC_000913 | 1,502,772 | 0 | G | A | 28.8% | 209.4 / 41.0 | 139 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 4,427,822 | 0 | C | A | 28.7% | 207.2 / 14.2 | 122 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 3,269,948 | 0 | T | C | 26.5% | 189.5 / 10.6 | 98 | intergenic (+346/+268) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 3,054,894 | 0 | G | T | 26.5% | 134.0 / 13.2 | 83 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 320,845 | 0 | C | A | 26.4% | 136.2 / 10.4 | 87 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 1,502,770 | 0 | T | C | 25.2% | 245.7 / 34.1 | 139 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 834,674 | 0 | C | A | 25.0% | 177.8 / 13.0 | 92 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 1,272,420 | 0 | C | A | 24.8% | 204.2 / 13.7 | 117 | intergenic (+71/‑87) | chaB/chaC | putative cation transport regulator ChaB/glutathione‑specific gamma‑glutamylcyclotransferase |
| * | NC_000913 | 2,365,840 | 0 | T | G | 24.6% | 237.2 / 10.0 | 134 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 3,181,552 | 0 | C | A | 24.5% | 214.1 / 10.4 | 99 | R378R (CGG→AGG) | ygiC | putative acid‑‑amine ligase YgiC |
| * | NC_000913 | 1,334,966 | 0 | A | C | 24.5% | 259.0 / 16.8 | 144 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 74 (0.840) | 10 (0.160) | 10/412 | 3.7 | 15.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 55 (0.890) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3648146 | 95 (1.070) | 12 (0.170) | 11/474 | 4.0 | 12.0% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 100 (1.410) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 1287329 | 51 (0.580) | 9 (0.140) | 8/416 | 4.4 | 21.2% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 31 (0.500) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 3469040 | 94 (1.060) | 11 (0.130) | 11/550 | 4.7 | 10.5% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 99 (1.200) | coding (510/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 3648156 | 96 (1.080) | 13 (0.150) | 11/580 | 4.9 | 10.5% | intergenic (+12/‑138) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648388 = | 126 (1.450) | intergenic (+13/‑140) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2818275 | 54 (0.610) | 7 (0.110) | 7/432 | 4.9 | 12.9% | intergenic (‑1/+198) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818551 = | 55 (0.850) | intergenic (‑2/+2) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 781322 | 71 (0.800) | 8 (0.100) | 8/512 | 5.3 | 9.6% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 89 (1.160) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4542690 | 140 (1.580) | 10 (0.120) | 9/572 | 5.5 | 7.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 111 (1.290) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 696506 | 73 (0.820) | 12 (0.160) +45 bp |
7/500 | 5.6 | 15.0% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 88 (0.990) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 10 (0.110) | 9/590 | 5.7 | 13.7% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2867356 | 63 (0.710) | coding (196/993 nt) | rpoS | RNA polymerase sigma factor RpoS | |||||