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 46 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,622,422 | 0 | C | G | 77.3% | 33.8 / 12.3 | 23 | A1077A (GCC→GCG) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 339,986 | 0 | G | A | 75.0% | 47.6 / 13.3 | 32 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 67.7% | 42.4 / 17.2 | 34 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 2,171,384 | 0 | A | C | 64.0% | 0.0 / 18.6 | 25 | K285Q (AAG→CAG) | insF5 | IS3 element protein InsF |
| * | NC_000913 | 1,820,763 | 0 | G | T | 38.4% | 153.9 / 10.4 | 112 | S151Y (TCC→TAC) | chbC | N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component |
| * | NC_000913 | 2,288,418 | 0 | G | T | 36.6% | 235.4 / 39.0 | 155 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.4% | 211.8 / 23.2 | 131 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 332,975 | 0 | C | A | 33.1% | 210.5 / 15.1 | 136 | S202* (TCG→TAG) | pdeL | DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 442,025 | 0 | C | A | 32.4% | 200.4 / 10.9 | 111 | L159L (CTC→CTA) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 2,856,087 | 0 | G | T | 32.0% | 171.4 / 10.9 | 103 | E584* (GAG→TAG) | fhlA | DNA‑binding transcriptional activator FhlA |
| * | NC_000913 | 2,326,713 | 0 | C | A | 31.8% | 190.6 / 14.2 | 110 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 847,955 | 0 | G | A | 31.6% | 197.5 / 64.7 | 158 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,360,965 | 0 | C | A | 30.9% | 308.9 / 29.8 | 162 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,477,265 | 0 | A | C | 30.4% | 134.0 / 17.9 | 79 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,427,822 | 0 | C | A | 29.3% | 301.4 / 15.1 | 164 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 1,922,815 | 0 | C | A | 28.9% | 223.1 / 12.1 | 121 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,296,268 | 0 | T | C | 28.6% | 36.4 / 15.2 | 28 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,767,444 | 0 | C | A | 28.2% | 238.2 / 14.2 | 103 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,272,420 | 0 | C | A | 27.9% | 195.5 / 12.7 | 111 | intergenic (+71/‑87) | chaB/chaC | putative cation transport regulator ChaB/glutathione‑specific gamma‑glutamylcyclotransferase |
| * | NC_000913 | 141,849 | 0 | C | A | 27.8% | 226.9 / 17.5 | 115 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| Marginal new junction evidence (lowest skew 10 of 38 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1293199 | 118 (1.120) | 24 (0.230) | 22/590 | 3.5 | 16.9% | intergenic (‑277/‑328) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| ? | NC_000913 | 1299499 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 696741 | 66 (0.630) | 16 (0.210) | 12/434 | 4.2 | 22.1% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 64 (0.830) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 24 (0.230) | 16/590 | 4.7 | 16.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1102451 | 123 (1.170) | coding (91/390 nt) | csgE | curli assembly component CsgE | |||||
| * | ? | NC_000913 | = 2653419 | 102 (0.970) | 13 (0.130) | 13/540 | 5.0 | 11.5% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 106 (1.100) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 676306 | 109 (1.040) | 21 (0.200) | 14/590 | 5.2 | 16.2% | coding (242/978 nt) | ybeQ | Sel1 repeat‑containing protein YbeQ |
| ? | NC_000913 | 687851 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2558698 | 82 (0.780) | 14 (0.140) | 13/574 | 5.3 | 14.4% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 87 (0.850) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | 1293196 = | 129 (1.230) | 15 (0.140) | 13/590 | 5.4 | 10.4% | intergenic (‑274/‑331) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2653549 | 97 (0.920) | 10 (0.100) | 10/558 | 6.1 | 9.0% | intergenic (‑94/‑306) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653872 = | 111 (1.110) | noncoding (18/304 nt) | ryfA | small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 1102448 = | 122 (1.160) | 10 (0.100) | 10/580 | 6.3 | 7.7% | coding (94/390 nt) | csgE | curli assembly component CsgE |
| ? | NC_000913 | 1396044 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4606166 | 78 (0.740) | 5 (0.070) | 5/412 | 6.5 | 7.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 64 (0.870) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||