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 121 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 70,371 | 0 | T | C | 55.1% | 60.2 / inf | 236 | intergenic (‑323/‑16) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,740 | 0 | T | G | 53.1% | 49.9 / 182.6 | 128 | G118G (GGT→GGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,175 | 0 | A | G | 51.3% | ‑4.6 / 237.1 | 149 | R263R (CGA→CGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,289 | 0 | G | T | 51.2% | ‑2.5 / inf | 216 | intergenic (‑241/‑98) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,214 | 0 | T | C | 51.1% | 7.2 / 224.5 | 139 | F276F (TTT→TTC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,322 | 0 | C | T | 49.6% | 12.1 / 231.5 | 139 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 70,434 | 0 | C | T | 49.1% | 3.9 / inf | 229 | N16N (AAC→AAT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,335 | 0 | C | A | 48.3% | 25.0 / 216.3 | 147 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,337 | 0 | G | A | 48.2% | 6.3 / 236.0 | 143 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 71,085 | 0 | T | C | 47.5% | 29.6 / 218.5 | 143 | S233S (AGT→AGC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,079 | 0 | C | T | 47.2% | 12.1 / 224.3 | 143 | R231R (CGC→CGT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,082 | 0 | T | C | 46.9% | 42.0 / 213.9 | 145 | I232I (ATT→ATC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,109 | 0 | T | C | 46.5% | 43.2 / 215.8 | 144 | T241T (ACT→ACC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,581 | 0 | C | T | 46.2% | 6.7 / 251.2 | 156 | V65V (GTC→GTT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,291 | 0 | G | A | 44.3% | 49.9 / 140.9 | 124 | R153Q (CGG→CAG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,289 | 0 | A | G | 44.2% | 64.8 / 141.7 | 121 | K152K (AAA→AAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,275 | 0 | G | A | 43.5% | 26.2 / 176.9 | 124 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,290 | 0 | C | A | 43.5% | 50.0 / 162.0 | 124 | R153R (CGG→AGG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,295 | 0 | T | C | 43.5% | 53.7 / 167.7 | 124 | D154D (GAT→GAC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,301 | 0 | C | T | 43.5% | 46.4 / 165.8 | 124 | I156I (ATC→ATT) | nohD | putative DNA‑packaging protein NohD |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3648146 | 95 (1.060) | 17 (0.240) | 17/472 | 2.6 | 16.4% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 97 (1.350) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 696741 | 92 (1.030) | 12 (0.180) | 8/432 | 4.5 | 16.6% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 53 (0.810) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 1207800 = | 29 (0.320) | 13 (0.150) +A |
12/586 | 4.7 | 31.0% | coding (300/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209610 = | 29 (0.320) | intergenic (‑491/‑75) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 4094350 | 78 (0.870) | 9 (0.120) | 9/506 | 4.9 | 12.7% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 57 (0.740) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 3469040 | 83 (0.930) | 10 (0.120) | 9/548 | 5.3 | 11.1% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 83 (1.000) | coding (510/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 2357730 | 118 (1.320) | 10 (0.130) | 8/508 | 5.3 | 9.0% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 100 (1.300) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1286906 | 50 (0.560) | 11 (0.130) | 9/548 | 5.3 | 18.7% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 49 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2357664 | 128 (1.430) | 8 (0.090) | 8/566 | 5.8 | 6.6% | coding (761/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357848 = | 102 (1.190) | intergenic (+45/+194) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | 781577 = | 46 (0.510) | 9 (0.100) +GAAG |
8/580 | 5.9 | 12.6% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 81 (0.910) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 4542690 | 148 (1.660) | 7 (0.080) | 7/570 | 6.2 | 5.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 110 (1.270) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||