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 124 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 | 47.2% | 84.8 / inf | 176 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 1,097,158 | 0 | C | T | 42.9% | 21.9 / 57.0 | 49 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,433,340 | 0 | G | T | 41.8% | 91.8 / 18.2 | 79 | S196Y (TCC→TAC) | accD | acetyl‑CoA carboxyltransferase subunit beta |
| * | NC_000913 | 581,322 | 0 | C | T | 39.0% | 88.5 / 183.1 | 148 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,335 | 0 | C | A | 37.4% | 171.3 / 147.7 | 156 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,381 | 0 | A | G | 37.0% | 149.1 / 176.5 | 154 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,337 | 0 | G | A | 36.8% | 133.0 / 176.6 | 155 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 4,136,467 | 0 | A | C | 36.8% | 98.8 / 24.1 | 68 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 58,065 | 0 | C | A | 36.8% | 176.9 / 24.9 | 117 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 581,380 | 0 | C | G | 36.4% | 181.0 / 186.1 | 154 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.5% | 189.6 / 41.3 | 111 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,611,507 | 0 | G | T | 33.3% | 183.2 / 13.3 | 108 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 1,334,966 | 0 | A | C | 33.1% | 188.3 / 35.8 | 157 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 31.7% | 133.2 / 33.5 | 102 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 581,388 | 0 | G | A | 31.2% | 169.7 / 130.3 | 138 | intergenic (+9/‑146) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,476 | 0 | G | C | 31.1% | 186.7 / 138.0 | 138 | intergenic (+97/‑58) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 2,767,445 | 0 | C | A | 31.1% | 249.2 / 23.1 | 132 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 581,392 | 0 | T | C | 30.9% | 194.1 / 128.2 | 139 | intergenic (+13/‑142) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,275 | 0 | G | A | 30.9% | 148.0 / 113.5 | 123 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 847,955 | 0 | G | A | 30.7% | 194.9 / 67.9 | 141 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| Marginal new junction evidence (lowest skew 10 of 65 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 28 (0.250) | 24/596 | 4.0 | 21.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2230311 = | 104 (0.910) | coding (75/948 nt) | dusC | tRNA‑dihydrouridine(16) synthase | |||||
| * | ? | NC_000913 | = 16659 | NA (NA) | 26 (0.230) | 24/598 | 4.1 | NA | noncoding (1273/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 270541 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1287329 | 80 (0.700) | 12 (0.150) | 11/424 | 5.3 | 19.2% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 44 (0.540) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 4606166 | 98 (0.860) | 11 (0.140) | 10/420 | 5.6 | 14.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 64 (0.800) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 270541 = | NA (NA) | 16 (0.140) | 15/598 | 6.1 | 13.7% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2230312 | 101 (0.890) | coding (74/948 nt) | dusC | tRNA‑dihydrouridine(16) synthase | |||||
| * | ? | NC_000913 | = 609351 | NA (NA) | 15 (0.130) | 14/590 | 6.3 | 13.5% | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 2904080 | 96 (0.850) | intergenic (+706/+667) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | 1838216 = | 57 (0.500) | 17 (0.150) | 14/598 | 6.4 | 22.7% | coding (1005/1536 nt) | ynjC | putative ABC transporter membrane subunit YnjC |
| ? | NC_000913 | = 1838223 | 59 (0.520) | coding (1012/1536 nt) | ynjC | putative ABC transporter membrane subunit YnjC | |||||
| * | ? | NC_000913 | 971728 = | 136 (1.200) | 15 (0.130) | 14/594 | 6.4 | 9.9% | intergenic (+130/‑24) | kdsB/ycbJ | 3‑deoxy‑manno‑octulosonate cytidylyltransferase/putative phosphotransferase YcbJ |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 891857 = | 82 (0.720) | 19 (0.170) | 14/598 | 6.4 | 18.8% | coding (674/723 nt) | nfsA | NADPH‑dependent nitro/quinone reductase NfsA |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 10 (0.110) +70 bp |
9/458 | 6.5 | 65.1% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2238956 | 7 (0.060) | coding (334/1521 nt) | mglA | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit | |||||