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 64 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,304,522 | 0 | G | T | 78.6% | 23.3 / 14.4 | 28 | intergenic (+129/+586) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 2,304,537 | 0 | A | G | 76.7% | 26.6 / 15.0 | 30 | intergenic (+144/+571) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 2,304,523 | 0 | G | C | 75.0% | 24.0 / 19.2 | 29 | intergenic (+130/+585) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 2,304,540 | 0 | C | T | 68.8% | 13.6 / 22.3 | 32 | intergenic (+147/+568) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 339,986 | 0 | G | A | 58.3% | 19.7 / 40.7 | 36 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 2,304,549 | 0 | C | T | 55.6% | ‑5.2 / 41.4 | 37 | intergenic (+156/+559) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 339,979 | 0 | G | A | 52.8% | 10.1 / 45.5 | 36 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 2,304,567 | 0 | C | T | 52.6% | 5.5 / 48.4 | 38 | intergenic (+174/+541) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 2,304,575 | 0 | G | A | 51.3% | 11.4 / 50.8 | 38 | intergenic (+182/+533) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | NC_000913 | 339,992 | 0 | C | . | 38.9% | 65.4 / 59.6 | 36 | coding (224/321 nt) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 58,065 | 0 | C | A | 38.5% | 143.5 / 36.8 | 117 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.6% | 288.5 / 43.3 | 185 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 799,484 | 0 | C | A | 33.7% | 148.8 / 10.5 | 92 | S300* (TCG→TAG) | pgl | 6‑phosphogluconolactonase |
| * | NC_000913 | 1,823,018 | 0 | C | A | 32.0% | 179.8 / 11.8 | 122 | L187L (CTC→CTA) | nadE | NH3‑dependent NAD(+) synthetase |
| * | NC_000913 | 2,767,444 | 0 | C | A | 30.5% | 311.7 / 11.1 | 132 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 866,319 | 0 | C | A | 30.3% | 188.5 / 13.8 | 123 | E16* (GAG→TAG) | moeA | molybdopterin molybdotransferase |
| * | NC_000913 | 847,955 | 0 | G | A | 29.8% | 252.5 / 67.8 | 188 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,722,838 | 0 | G | T | 29.7% | 280.1 / 15.5 | 148 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 2,472,817 | 0 | C | A | 29.7% | 237.8 / 15.2 | 119 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 42,395 | 0 | G | T | 29.6% | 224.2 / 11.2 | 142 | intergenic (‑464/‑8) | caiT/fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| Marginal new junction evidence (lowest skew 10 of 54 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3133052 = | 101 (0.810) | 39 (0.320) | 25/576 | 3.2 | 26.3% | coding (161/759 nt) | yghR | putative ATP‑binding protein YghR |
| ? | NC_000913 | = 3306041 | 120 (0.990) | coding (1820/1890 nt) | deaD | ATP‑dependent RNA helicase DeaD | |||||
| * | ? | NC_000913 | 4542682 = | 213 (1.720) | 28 (0.230) | 22/572 | 3.6 | 14.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 139 (1.160) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 225 (1.810) | 25 (0.210) | 20/572 | 4.0 | 12.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 138 (1.150) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648146 | 156 (1.260) | 13 (0.130) | 13/474 | 4.6 | 8.9% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 141 (1.410) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4606166 | 109 (0.880) | 11 (0.130) | 8/412 | 5.5 | 13.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 68 (0.790) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2947467 | 97 (0.780) | 9 (0.100) | 8/424 | 5.6 | 11.8% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 65 (0.730) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2653419 | 122 (0.980) | 13 (0.110) | 11/540 | 5.8 | 9.7% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 130 (1.140) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 780918 | 102 (0.820) | 9 (0.100) | 8/438 | 5.8 | 10.8% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 73 (0.790) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2357730 | 153 (1.230) | 7 (0.070) | 7/510 | 7.0 | 5.2% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 124 (1.160) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | 781577 = | 81 (0.650) | 8 (0.070) +GAAG |
8/582 | 7.2 | 7.3% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 125 (1.010) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||