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 119 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 71,079 | 0 | C | T | 57.7% | 109.4 / 220.4 | 168 | R231R (CGC→CGT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,214 | 0 | T | C | 57.3% | 61.6 / 287.6 | 199 | F276F (TTT→TTC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,082 | 0 | T | C | 56.5% | 66.5 / 238.9 | 169 | I232I (ATT→ATC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,085 | 0 | T | C | 56.2% | 60.9 / 249.5 | 170 | S233S (AGT→AGC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,109 | 0 | T | C | 55.8% | 56.7 / 265.2 | 181 | T241T (ACT→ACC) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 71,175 | 0 | A | G | 55.3% | 71.5 / 268.6 | 190 | R263R (CGA→CGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,289 | 0 | G | T | 52.3% | 6.4 / inf | 218 | intergenic (‑241/‑98) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,740 | 0 | T | G | 51.9% | 55.1 / 221.1 | 154 | G118G (GGT→GGG) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,371 | 0 | T | C | 51.7% | ‑2.7 / inf | 231 | intergenic (‑323/‑16) | araB/araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 70,434 | 0 | C | T | 50.4% | 9.1 / inf | 221 | N16N (AAC→AAT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 190,843 | 0 | C | A | 49.4% | 85.3 / 10.6 | 87 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 581,322 | 0 | C | T | 49.3% | 10.1 / 237.0 | 142 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 70,581 | 0 | C | T | 49.1% | 3.8 / 268.3 | 159 | V65V (GTC→GTT) | araC | DNA‑binding transcriptional dual regulator AraC |
| * | NC_000913 | 581,335 | 0 | C | A | 48.6% | 42.3 / 205.8 | 148 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,337 | 0 | G | A | 48.6% | ‑4.6 / 241.7 | 148 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,381 | 0 | A | G | 46.2% | 52.5 / 230.1 | 156 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,476 | 0 | G | C | 45.7% | 24.4 / 204.5 | 131 | intergenic (+97/‑58) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,380 | 0 | C | G | 45.5% | 73.9 / 237.5 | 157 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,437 | 0 | G | A | 45.1% | 35.1 / 199.5 | 133 | intergenic (+58/‑97) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,455 | 0 | G | A | 45.1% | 34.4 / 199.7 | 133 | intergenic (+76/‑79) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| Marginal new junction evidence (lowest skew 10 of 23 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2653393 | 79 (0.850) | 11 (0.120) | 10/580 | 5.8 | 10.2% | noncoding (63/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653720 = | 116 (1.260) | intergenic (‑265/‑135) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 1287160 | 59 (0.640) | 10 (0.110) | 9/568 | 6.0 | 13.2% | noncoding (77/171 nt) coding (17/90 nt) |
rttR tpr |
small RNA RttR protamine‑like protein |
| ? | NC_000913 | 1287458 = | 74 (0.820) | intergenic (‑130/+80) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | 781577 = | 65 (0.700) | 12 (0.130) +GAAG |
9/578 | 6.1 | 13.6% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 90 (0.970) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 696567 | 95 (1.030) | 7 (0.080) | 7/562 | 6.7 | 7.2% | noncoding (50/75 nt) | glnV | tRNA‑Gln |
| ? | NC_000913 | 696690 = | 90 (1.010) | noncoding (51/77 nt) | metU | tRNA‑Met | |||||
| * | ? | NC_000913 | 4542682 = | 131 (1.410) | 7 (0.080) | 7/568 | 6.8 | 5.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 121 (1.350) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 732408 = | 45 (0.490) | 7 (0.080) | 6/562 | 7.2 | 14.0% | coding (2826/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | = 3621836 | NA (NA) | coding (2645/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 732239 | 57 (0.620) | 7 (0.080) | 6/562 | 7.2 | 12.5% | coding (2657/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 732420 = | 43 (0.480) | coding (2838/4194 nt) | rhsC | rhs element protein RhsC | |||||
| * | ? | NC_000913 | = 2877791 | 69 (0.740) | 4 (0.050) | 4/550 | 8.1 | 6.2% | intergenic (+173/+778) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| ? | NC_000913 | 2878097 = | 56 (0.640) | intergenic (+479/+472) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 | |||||
| * | ? | NC_000913 | = 4606238 | 60 (0.650) | 3 (0.040) | 3/504 | 8.2 | 5.4% | noncoding (49/87 nt) | leuP | tRNA‑Leu |
| ? | NC_000913 | 4606354 = | 54 (0.680) | noncoding (48/87 nt) | leuQ | tRNA‑Leu | |||||
| * | ? | NC_000913 | = 4542690 | 141 (1.520) | 4 (0.040) | 4/568 | 8.3 | 3.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 121 (1.350) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||