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 163 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 581,335 | 0 | C | A | 79.8% | 917.3 / 268.8 | 453 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 566,651 | 0 | T | C | 79.6% | 1062.6 / 261.3 | 466 | intergenic (‑673/‑33) | intD/renD | putative integrase/protein RenD |
| * | NC_000913 | 566,565 | 0 | A | G | 79.5% | 831.6 / 206.1 | 381 | intergenic (‑587/‑119) | intD/renD | putative integrase/protein RenD |
| * | NC_000913 | 566,570 | 0 | A | C | 79.4% | 947.6 / 202.7 | 389 | intergenic (‑592/‑114) | intD/renD | putative integrase/protein RenD |
| * | NC_000913 | 581,381 | 0 | A | G | 79.3% | 1000.0 / 268.8 | 454 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,380 | 0 | C | G | 78.7% | 1009.7 / 302.9 | 455 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 1,951,386 | 0 | C | T | 77.5% | 584.9 / 150.2 | 276 | L185L (CTC→CTT) | yecD | isochorismatase family protein YecD |
| * | NC_000913 | 1,951,412 | 0 | A | G | 76.3% | 505.1 / 163.9 | 254 | L6L (CTA→CTG) | yecE | DUF72 domain‑containing protein YecE |
| * | NC_000913 | 581,416 | 0 | A | G | 75.8% | 687.0 / 251.5 | 364 | intergenic (+37/‑118) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,275 | 0 | G | A | 75.8% | 697.3 / 223.3 | 334 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,394 | 0 | T | C | 75.5% | 669.3 / 267.2 | 367 | intergenic (+15/‑140) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,398 | 0 | C | G | 75.4% | 762.1 / 290.4 | 366 | intergenic (+19/‑136) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,397 | 0 | T | C | 75.3% | 676.9 / 261.4 | 365 | intergenic (+18/‑137) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,412 | 0 | G | T | 75.3% | 633.5 / 267.4 | 366 | intergenic (+33/‑122) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,290 | 0 | C | A | 75.3% | 572.1 / 244.2 | 336 | R153R (CGG→AGG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,291 | 0 | G | A | 75.3% | 590.4 / 215.1 | 337 | R153Q (CGG→CAG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,301 | 0 | C | T | 75.3% | 660.6 / 236.0 | 336 | I156I (ATC→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,392 | 0 | T | C | 75.2% | 686.3 / 264.5 | 367 | intergenic (+13/‑142) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,413 | 0 | C | T | 75.2% | 735.6 / 258.1 | 367 | intergenic (+34/‑121) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,428 | 0 | G | T | 75.2% | 655.7 / 271.0 | 367 | intergenic (+49/‑106) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 156 (1.570) | 24 (0.330) | 17/442 | 2.3 | 16.9% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 120 (1.640) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 780629 | 167 (1.680) | 15 (0.200) | 13/446 | 3.1 | 12.4% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 87 (1.180) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 4606166 | 93 (0.940) | 10 (0.140) | 10/420 | 3.5 | 14.0% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 58 (0.830) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 4542682 = | 142 (1.430) | 15 (0.160) | 13/580 | 4.0 | 10.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 131 (1.360) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 696504 | 167 (1.680) | 11 (0.120) | 10/540 | 4.4 | 6.6% | noncoding (1/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696940 = | 161 (1.800) | intergenic (‑1/+23) | glnU/leuW | tRNA‑Gln/tRNA‑Leu | |||||
| * | ? | NC_000913 | = 4542690 | 164 (1.650) | 11 (0.110) | 10/580 | 4.7 | 7.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 131 (1.360) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4094350 | 77 (0.780) | 6 (0.070) | 6/516 | 5.5 | 9.5% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 48 (0.560) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 2653419 | 76 (0.770) | 8 (0.090) | 6/548 | 5.7 | 10.0% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 75 (0.820) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 781577 = | 136 (1.370) | 7 (0.070) +GAAG |
7/590 | 5.7 | 6.4% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 70 (0.710) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 349693 | 36 (0.360) | 5 (0.050) | 5/564 | 6.3 | 9.0% | intergenic (+121/‑319) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| ? | NC_000913 | 349973 = | 67 (0.720) | intergenic (+401/‑39) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase | |||||