mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 125 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 581,337 | 0 | G | A | 46.2% | 14.4 / 226.0 | 145 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,322 | 0 | C | T | 45.3% | 6.5 / 211.3 | 138 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,335 | 0 | C | A | 45.2% | 79.2 / 180.9 | 146 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,381 | 0 | A | G | 41.5% | 96.5 / 175.7 | 135 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,380 | 0 | C | G | 41.3% | 102.5 / 178.2 | 135 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,286 | 0 | G | C | 41.2% | 75.8 / 157.5 | 121 | L151L (CTG→CTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,275 | 0 | G | A | 40.5% | 48.6 / 166.0 | 121 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,289 | 0 | A | G | 40.5% | 103.4 / 129.8 | 121 | K152K (AAA→AAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,290 | 0 | C | A | 40.5% | 95.1 / 137.2 | 121 | R153R (CGG→AGG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,291 | 0 | G | A | 40.5% | 69.4 / 137.2 | 121 | R153Q (CGG→CAG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,295 | 0 | T | C | 40.2% | 82.0 / 148.7 | 122 | D154D (GAT→GAC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,301 | 0 | C | T | 40.2% | 62.7 / 159.7 | 122 | I156I (ATC→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,259 | 0 | A | G | 39.1% | 80.7 / 137.4 | 115 | E142E (GAA→GAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,250 | 0 | T | C | 38.8% | 74.2 / 123.5 | 103 | R139R (CGT→CGC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,253 | 0 | T | C | 38.8% | 90.5 / 108.3 | 103 | F140F (TTT→TTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 58,065 | 0 | C | A | 38.0% | 115.4 / 36.1 | 92 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,427,992 | 0 | G | T | 37.2% | 130.3 / 14.0 | 102 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,911,533 | 0 | C | A | 36.0% | 181.8 / 19.7 | 125 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,990,480 | 0 | C | A | 35.5% | 204.2 / 33.0 | 138 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 581,241 | 0 | G | T | 35.2% | 123.0 / 99.6 | 105 | V136V (GTG→GTT) | nohD | putative DNA‑packaging protein NohD |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1287329 | 73 (0.760) | 11 (0.160) | 7/414 | 5.1 | 18.6% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 45 (0.670) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | 4542682 = | 142 (1.480) | 10 (0.110) | 10/570 | 5.6 | 6.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 135 (1.450) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 144 (1.500) | 13 (0.140) | 9/570 | 5.9 | 8.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 133 (1.430) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648156 | 91 (0.950) | 11 (0.120) | 9/578 | 6.0 | 11.2% | intergenic (+12/‑138) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648388 = | 85 (0.900) | intergenic (+13/‑140) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 1207800 = | 78 (0.810) | 8 (0.080) +A |
7/586 | 6.9 | 9.8% | coding (300/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209610 = | 69 (0.720) | intergenic (‑491/‑75) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1286906 | 66 (0.690) | 9 (0.100) | 6/548 | 7.0 | 12.3% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 67 (0.750) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2357742 | 111 (1.160) | 6 (0.070) | 6/566 | 7.1 | 5.3% | coding (839/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357938 = | 108 (1.170) | intergenic (+135/+104) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3095995 | 103 (1.080) | 5 (0.050) | 5/566 | 7.6 | 5.0% | coding (176/567 nt) | yggT | uncharacterized protein YggT |
| ? | NC_000913 | 3096266 = | 89 (0.970) | coding (447/567 nt) | yggT | uncharacterized protein YggT | |||||
| * | ? | NC_000913 | = 3130938 | NA (NA) | 5 (0.050) | 5/572 | 7.7 | 5.3% | noncoding (793/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3131418 = | 91 (0.950) | coding (991/1068 nt) | yghQ | putative transport protein YghQ | |||||
| * | ? | NC_000913 | = 2653386 | 83 (0.870) | 5 (0.050) +C |
5/586 | 7.8 | 5.1% | noncoding (70/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653714 = | 105 (1.100) | intergenic (‑259/‑141) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||