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 41 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,037,496 | 0 | A | T | 45.0% | 124.8 / inf | 189 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 39.6% | 109.5 / 49.6 | 106 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,445 | 0 | C | A | 38.7% | 181.4 / 32.2 | 111 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,611,507 | 0 | G | T | 37.8% | 97.3 / 10.6 | 82 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 3,054,886 | 0 | G | T | 37.1% | 137.4 / 47.1 | 106 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,888 | 0 | A | C | 36.2% | 173.0 / 13.8 | 106 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.8% | 144.3 / 28.8 | 89 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,427,822 | 0 | C | A | 32.0% | 259.2 / 21.8 | 147 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 1,470,627 | 0 | C | A | 31.9% | 231.3 / 15.0 | 119 | pseudogene (109/3495 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,767,449 | 0 | C | A | 31.9% | 239.6 / 11.5 | 117 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,812,509 | 0 | G | T | 31.1% | 234.4 / 30.3 | 135 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 3,841,663 | 0 | G | A | 29.8% | 103.4 / 16.7 | 67 | A26V (GCG→GTG) | nepI | purine ribonucleoside exporter |
| * | NC_000913 | 3,970,253 | 0 | G | T | 29.8% | 181.8 / 11.0 | 124 | E41* (GAG→TAG) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase |
| * | NC_000913 | 3,741,871 | 0 | G | T | 29.5% | 179.7 / 21.5 | 112 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 847,955 | 0 | G | A | 29.2% | 151.0 / 42.5 | 106 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,922,815 | 0 | C | A | 29.1% | 161.6 / 23.3 | 110 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 834,674 | 0 | C | A | 28.7% | 197.2 / 13.9 | 101 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 3,911,533 | 0 | C | A | 28.0% | 287.9 / 14.8 | 161 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,296,268 | 0 | T | C | 27.8% | 82.8 / 34.5 | 54 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,602,706 | 0 | C | A | 26.7% | 112.4 / 29.3 | 75 | G14G (GGG→GGT) | ftsE | cell division protein FtsE |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696469 | 127 (1.240) | 22 (0.220) +TAGAAT |
18/586 | 4.0 | 15.0% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696802 = | 127 (1.240) | noncoding (29/75 nt) | glnW | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 696741 | 137 (1.340) | 13 (0.170) | 8/442 | 5.3 | 11.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 106 (1.400) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 4606166 | 104 (1.020) | 6 (0.080) | 5/420 | 6.3 | 7.5% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 76 (1.060) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1287084 | 49 (0.480) | 8 (0.080) | 7/558 | 6.8 | 14.4% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 49 (0.510) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781322 | 107 (1.040) | 6 (0.070) | 6/520 | 6.9 | 4.9% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 141 (1.580) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 3648146 | 124 (1.210) | 5 (0.060) | 5/482 | 7.0 | 5.1% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 88 (1.070) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781016 | 102 (1.000) | 6 (0.070) | 6/524 | 7.0 | 4.9% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | NC_000913 | 781809 = | 144 (1.600) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 3270072 = | 54 (0.530) | 5 (0.050) +25 bp |
5/548 | 7.7 | 5.8% | intergenic (+470/+144) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 4137788 = | 122 (1.190) | intergenic (‑131/+144) | yijF/gldA | DUF1287 domain‑containing protein YijF/L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase | |||||
| * | ? | NC_000913 | = 2818275 | 47 (0.460) | 3 (0.040) | 3/440 | 7.7 | 4.9% | intergenic (‑1/+198) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818551 = | 83 (1.100) | intergenic (‑2/+2) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 2521006 | 71 (0.690) | 3 (0.040) | 3/446 | 7.7 | 5.6% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521127 = | 49 (0.640) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||