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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,304,567 | 0 | C | T | 77.8% | 29.7 / 11.5 | 27 | intergenic (+174/+541) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 2,304,575 | 0 | G | A | 69.6% | 17.4 / 11.1 | 23 | intergenic (+182/+533) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 4,037,496 | 0 | A | T | 46.7% | 86.0 / 296.0 | 152 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 39.8% | 105.8 / 45.0 | 103 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 39.4% | 139.1 / 42.5 | 94 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,922,815 | 0 | C | A | 38.5% | 117.6 / 41.1 | 130 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 190,843 | 0 | C | A | 37.4% | 123.5 / 12.0 | 91 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 1,427,992 | 0 | G | T | 32.8% | 162.2 / 21.3 | 122 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.4% | 161.7 / 32.2 | 102 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.9% | 235.3 / 26.6 | 144 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,490,240 | 0 | G | T | 31.8% | 192.0 / 17.5 | 132 | intergenic (‑54/+16) | yfdV/oxc | putative transport protein YfdV/oxalyl‑CoA decarboxylase |
| * | NC_000913 | 2,073,613 | 0 | G | T | 31.2% | 123.9 / 22.5 | 77 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 1,945,526 | 0 | G | T | 30.9% | 129.1 / 13.8 | 84 | P151T (CCT→ACT) | ruvA | Holliday junction branch migration complex subunit RuvA |
| * | NC_000913 | 58,065 | 0 | C | A | 30.7% | 198.7 / 21.1 | 101 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 847,955 | 0 | G | A | 30.4% | 191.8 / 46.3 | 127 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,756,353 | 0 | C | A | 29.7% | 183.0 / 11.1 | 101 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 1,611,507 | 0 | G | T | 29.5% | 189.1 / 11.6 | 105 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 1,812,509 | 0 | G | T | 29.5% | 305.4 / 21.2 | 156 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 4,136,467 | 0 | A | C | 29.0% | 137.4 / 13.6 | 72 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 3,841,663 | 0 | G | A | 28.6% | 119.0 / 21.6 | 63 | A26V (GCG→GTG) | nepI | purine ribonucleoside exporter |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 137 (1.290) | 34 (0.330) | 26/580 | 3.2 | 22.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 106 (1.030) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 126 (1.190) | 33 (0.320) | 23/580 | 3.8 | 22.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 107 (1.040) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 696741 | 71 (0.670) | 17 (0.220) | 14/442 | 4.3 | 22.3% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 66 (0.840) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1287329 | 83 (0.780) | 11 (0.150) | 10/424 | 5.3 | 18.2% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 40 (0.530) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 1286906 | 64 (0.600) | 12 (0.120) | 10/558 | 7.0 | 18.1% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 49 (0.500) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 696506 | 106 (1.000) | 8 (0.090) +45 bp |
6/508 | 8.2 | 8.5% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 96 (0.910) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | = 2518116 | 86 (0.810) | 5 (0.060) | 4/436 | 8.3 | 7.6% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 59 (0.760) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 781222 | 50 (0.470) | 4 (0.050) | 4/446 | 8.5 | 8.0% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 55 (0.700) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 1096961 = | 82 (0.770) | 5 (0.060) | 3/438 | 9.0 | 8.0% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 55 (0.710) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 1287084 | 67 (0.630) | 6 (0.060) | 5/558 | 9.3 | 9.7% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 49 (0.500) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||