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 58 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 847,955 | 0 | G | A | 37.2% | 91.0 / 78.1 | 129 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,823,018 | 0 | C | A | 37.1% | 147.3 / 10.7 | 97 | L187L (CTC→CTA) | nadE | NH3‑dependent NAD(+) synthetase |
| * | NC_000913 | 3,226,224 | 0 | G | T | 35.3% | 150.1 / 12.3 | 102 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| * | NC_000913 | 4,427,822 | 0 | C | A | 35.1% | 245.1 / 30.2 | 148 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 1,427,992 | 0 | G | T | 34.8% | 222.3 / 11.9 | 132 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,913,085 | 0 | G | T | 34.0% | 181.4 / 14.5 | 107 | L189L (CTC→CTA) | relA | GDP/GTP pyrophosphokinase |
| * | NC_000913 | 2,767,445 | 0 | C | A | 33.3% | 151.6 / 20.7 | 90 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,426,954 | 0 | G | T | 32.9% | 121.4 / 14.7 | 79 | intergenic (‑171/+4) | rrlD/alaU | 23S ribosomal RNA/tRNA‑Ala |
| * | NC_000913 | 3,911,533 | 0 | C | A | 32.7% | 230.8 / 21.0 | 150 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 147,802 | 0 | C | A | 32.4% | 171.3 / 12.1 | 111 | R279R (CGG→AGG) | rpnC | recombination‑promoting nuclease RpnC |
| * | NC_000913 | 265,217 | 0 | C | A | 31.6% | 208.2 / 13.2 | 114 | intergenic (‑11/+87) | yafX/ykfF | protein YafX/protein YkfF |
| * | NC_000913 | 58,065 | 0 | C | A | 31.5% | 207.7 / 16.1 | 111 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 2,767,447 | 0 | C | A | 30.9% | 205.6 / 11.4 | 98 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,990,480 | 0 | C | A | 30.3% | 256.2 / 14.0 | 152 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 1,902,613 | 0 | C | A | 29.9% | 228.3 / 18.0 | 117 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 2,767,443 | 0 | C | A | 29.7% | 180.9 / 14.8 | 91 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,922,815 | 0 | C | A | 29.6% | 215.8 / 20.9 | 125 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 141,849 | 0 | C | A | 29.4% | 243.9 / 18.5 | 137 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 1,015,488 | 0 | C | A | 29.0% | 251.8 / 15.6 | 148 | intergenic (+29/‑227) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| * | NC_000913 | 2,767,444 | 0 | C | A | 28.9% | 171.6 / 13.0 | 91 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| Marginal new junction evidence (lowest skew 10 of 33 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2357730 | 119 (1.130) | 12 (0.130) | 12/508 | 5.0 | 11.5% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 82 (0.910) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4606166 | 105 (1.000) | 8 (0.110) | 8/410 | 5.2 | 8.9% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 90 (1.230) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1287084 | 78 (0.740) | 14 (0.140) | 11/548 | 5.7 | 20.3% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 37 (0.380) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2653419 | 97 (0.930) | 8 (0.080) | 8/538 | 6.7 | 7.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 107 (1.120) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4295870 | 122 (1.160) | 9 (0.100) | 6/510 | 7.3 | 8.2% | intergenic (+76/+566) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296434 = | 95 (1.040) | intergenic (+640/+2) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 781446 | 70 (0.670) | 4 (0.050) | 4/432 | 7.4 | 6.6% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 61 (0.790) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 1411899 = | 139 (1.330) | 8 (0.080) | 6/536 | 7.6 | 5.7% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 140 (1.460) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | 781577 = | 72 (0.690) | 8 (0.080) +G |
7/586 | 7.6 | 10.4% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521129 | 66 (0.630) | intergenic (+3/‑44) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1286906 | 65 (0.620) | 7 (0.070) | 6/548 | 7.7 | 12.6% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 37 (0.380) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781322 | 65 (0.620) | 6 (0.070) | 5/510 | 7.8 | 7.4% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 94 (1.030) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||