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 59 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 65.2% | 38.4 / 46.4 | 46 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 62.2% | 29.2 / 47.8 | 46 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 730,118 | 0 | C | A | 58.6% | 3.2 / 74.3 | 58 | P179Q (CCG→CAG) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 2,799,800 | 0 | G | T | 57.9% | 48.3 / 168.9 | 121 | P65P (CCC→CCA) | ygaC | DUF2002 domain‑containing protein YgaC |
| * | NC_000913 | 3,423,854 | 1 | . | A | 51.4% | 50.0 / 80.4 | 35 | intergenic (‑67/+26) | rrfD/rrlD | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_000913 | 2,392,703 | 0 | C | A | 48.4% | 20.5 / 138.2 | 97 | Q113H (CAG→CAT) | nuoM | NADH:quinone oxidoreductase subunit M |
| * | NC_000913 | 3,054,886 | 0 | G | T | 42.0% | 117.1 / 49.2 | 100 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 41.6% | 115.0 / 31.9 | 89 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 339,992 | 0 | C | . | 35.6% | 89.3 / 67.2 | 46 | coding (224/321 nt) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 3,735,651 | 0 | C | A | 35.0% | 179.1 / 133.9 | 144 | R225S (CGC→AGC) | xylR | DNA‑binding transcriptional dual regulator XylR |
| * | NC_000913 | 58,065 | 0 | C | A | 34.9% | 177.1 / 28.6 | 109 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.3% | 129.7 / 32.5 | 99 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,444 | 0 | C | A | 34.2% | 242.7 / 11.2 | 120 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,445 | 0 | C | A | 33.1% | 240.6 / 16.3 | 120 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,837,288 | 0 | C | A | 32.1% | 84.0 / 39.6 | 56 | P26Q (CCG→CAG) | ynjC | putative ABC transporter membrane subunit YnjC |
| * | NC_000913 | 2,767,449 | 0 | C | A | 31.2% | 266.0 / 11.9 | 129 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,051,943 | 0 | C | A | 31.1% | 126.0 / 67.6 | 103 | L2336M (CTG→ATG) | yeeJ | inverse autotransporter adhesin |
| * | NC_000913 | 1,922,815 | 0 | C | A | 30.9% | 144.7 / 19.5 | 94 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,249,810 | 0 | C | A | 29.9% | 211.9 / 11.5 | 107 | P86Q (CCG→CAG) | malM | maltose regulon periplasmic protein |
| * | NC_000913 | 4,296,191 | 0 | A | C | 29.7% | 40.4 / 24.1 | 37 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 71 (0.680) | 12 (0.160) | 9/442 | 5.2 | 17.8% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 58 (0.750) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1286906 | 71 (0.680) | 14 (0.140) | 12/558 | 5.4 | 18.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 57 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4392437 | 95 (0.910) | 7 (0.090) | 7/442 | 5.9 | 8.0% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 91 (1.180) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 4606166 | 115 (1.100) | 5 (0.070) | 5/420 | 6.6 | 6.0% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 75 (1.020) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781222 | 50 (0.480) | 4 (0.050) | 4/446 | 7.5 | 9.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 39 (0.500) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2947467 | 96 (0.920) | 4 (0.050) | 3/432 | 7.9 | 5.5% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 67 (0.890) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | 1096961 = | 80 (0.770) | 3 (0.040) | 3/438 | 8.0 | 5.3% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 48 (0.630) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 3469040 | 95 (0.910) | 5 (0.050) | 5/558 | 8.1 | 5.1% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 98 (1.010) | coding (510/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 1287084 | 64 (0.610) | 5 (0.050) | 4/558 | 8.7 | 7.9% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 57 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2357730 | 106 (1.020) | 3 (0.030) | 3/518 | 8.9 | 3.1% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 98 (1.080) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||