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 35 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,509,586 | 0 | A | C | 54.4% | 28.8 / 148.0 | 126 | pseudogene (108/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,592 | 0 | G | A | 44.3% | 43.0 / 129.7 | 122 | pseudogene (114/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,428 | 0 | A | G | 42.7% | 60.5 / 149.6 | 145 | pseudogene (420/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,487 | 0 | A | G | 42.4% | 62.2 / 159.0 | 144 | pseudogene (9/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,463 | 0 | T | G | 42.1% | 79.2 / 117.9 | 142 | pseudogene (455/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,037,496 | 0 | A | T | 41.7% | 45.8 / 88.3 | 72 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 4,509,416 | 0 | T | C | 41.4% | 56.4 / 146.5 | 140 | pseudogene (408/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,623 | 0 | G | A | 41.3% | 62.9 / 101.5 | 109 | pseudogene (145/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,655 | 0 | T | G | 41.0% | 42.6 / 104.5 | 101 | pseudogene (177/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,562 | 0 | T | C | 40.8% | 82.0 / 119.4 | 134 | pseudogene (84/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,544 | 0 | G | A | 39.7% | 111.3 / 124.4 | 142 | pseudogene (66/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,556 | 0 | T | C | 39.7% | 91.8 / 120.4 | 137 | pseudogene (78/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,632 | 0 | A | G | 39.0% | 59.6 / 89.5 | 104 | pseudogene (154/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,628 | 0 | A | G | 38.8% | 70.3 / 95.0 | 103 | pseudogene (150/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,537 | 0 | G | A | 38.4% | 108.2 / 121.3 | 140 | pseudogene (59/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,524 | 0 | C | T | 37.8% | 130.7 / 124.9 | 149 | pseudogene (46/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,637 | 0 | C | T | 37.8% | 66.0 / 89.7 | 104 | pseudogene (159/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,633 | 0 | C | T | 37.2% | 78.6 / 85.1 | 104 | pseudogene (155/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,630 | 0 | C | T | 37.0% | 72.6 / 84.8 | 103 | pseudogene (152/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,640 | 0 | T | C | 36.9% | 82.5 / 85.6 | 105 | pseudogene (162/315 nt) | insO | IS911B regulator fragment |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 5 (0.080) | 5/482 | 4.0 | 8.6% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3368689 | 53 (0.880) | coding (863/1128 nt) | yhcG | DUF1016 domain‑containing protein YhcG | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 4 (0.070) | 4/482 | 4.3 | 10.3% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4434636 | 35 (0.580) | coding (1930/1944 nt) | cpdB | 2',3'‑cyclic‑nucleotide 2'‑phosphodiesterase/3'‑nucleotidase | |||||
| * | ? | NC_000913 | = 458795 | 26 (0.440) | 4 (0.070) | 4/474 | 4.3 | 13.3% | intergenic (+95/‑93) | clpX/lon | ATP‑dependent Clp protease ATP‑binding subunit ClpX/Lon protease |
| ? | NC_000913 | = 609351 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 725618 | 107 (1.770) | 3 (0.050) | 3/466 | 4.6 | 2.9% | coding (1419/2049 nt) | kdpB | K(+) transporting P‑type ATPase subunit KdpB |
| ? | NC_000913 | 726093 = | 97 (1.660) | coding (944/2049 nt) | kdpB | K(+) transporting P‑type ATPase subunit KdpB | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 3 (0.050) | 3/482 | 4.7 | 8.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4348862 = | 31 (0.510) | intergenic (‑118/+453) | dcuB/dcuR | anaerobic C4‑dicarboxylate transporter DcuB/DNA‑binding transcriptional activator DcuR | |||||
| * | ? | NC_000913 | = 1584241 | 32 (0.530) | 3 (0.050) | 3/478 | 4.7 | 5.0% | coding (2246/2280 nt) | ydeP | putative oxidoreductase YdeP |
| ? | NC_000913 | 3730285 = | 82 (1.370) | coding (481/1323 nt) | xylA | xylose isomerase | |||||
| * | ? | NC_000913 | = 491933 | 104 (1.730) | 3 (0.050) | 3/474 | 4.7 | 3.0% | coding (522/552 nt) | apt | adenine phosphoribosyltransferase |
| ? | NC_000913 | = 492136 | 93 (1.570) | coding (45/1284 nt) coding (45/1932 nt) |
dnaX dnaX |
DNA polymerase III subunit tau DNA polymerase III subunit tau |
|||||
| * | ? | NC_000913 | = 26533 | 74 (1.230) | 4 (0.070) +CC |
3/478 | 4.7 | 4.9% | coding (257/951 nt) | ispH | 4‑hydroxy‑3‑methylbut‑2‑enyl diphosphate reductase |
| ? | NC_000913 | = 4363972 | 82 (1.360) | coding (1071/1698 nt) | dsbD | thiol‑disulfide exchange protein DsbD | |||||