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 40 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,037,496 | 0 | A | T | 48.6% | 51.2 / 294.0 | 147 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 58,065 | 0 | C | A | 37.4% | 136.4 / 22.2 | 99 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 320,845 | 0 | C | A | 36.7% | 86.9 / 12.3 | 79 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 2,073,613 | 0 | G | T | 35.9% | 118.2 / 10.9 | 78 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 3,669,715 | 0 | G | T | 35.1% | 153.2 / 15.3 | 111 | E42* (GAG→TAG) | treF | cytoplasmic trehalase |
| * | NC_000913 | 1,351,463 | 0 | C | A | 35.1% | 80.9 / 11.4 | 77 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 2,288,418 | 0 | G | T | 33.9% | 187.7 / 16.7 | 118 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,911,533 | 0 | C | A | 33.3% | 171.7 / 15.4 | 114 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 85,651 | 0 | G | T | 32.3% | 185.0 / 13.5 | 130 | E8* (GAG→TAG) | ilvI | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| * | NC_000913 | 2,427,716 | 0 | C | A | 31.1% | 222.0 / 10.4 | 106 | E26* (GAG→TAG) | argT | lysine/arginine/ornithine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,272,420 | 0 | C | A | 31.1% | 157.5 / 16.4 | 103 | intergenic (+71/‑87) | chaB/chaC | putative cation transport regulator ChaB/glutathione‑specific gamma‑glutamylcyclotransferase |
| * | NC_000913 | 442,025 | 0 | C | A | 30.0% | 159.4 / 11.1 | 90 | L159L (CTC→CTA) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 1,502,770 | 0 | T | C | 29.9% | 165.4 / 36.9 | 107 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 2,767,444 | 0 | C | A | 29.7% | 284.6 / 21.1 | 128 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,447 | 0 | C | A | 29.3% | 313.1 / 15.8 | 133 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 141,849 | 0 | C | A | 29.1% | 215.6 / 10.2 | 117 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 4,540,411 | 0 | C | A | 28.4% | 306.0 / 14.2 | 169 | intergenic (‑910/‑546) | nanC/fimB | N‑acetylneuraminate outer membrane channel/Type 1 fimbriae regulatory protein FimB |
| * | NC_000913 | 848,028 | 0 | G | T | 27.8% | 217.7 / 21.9 | 126 | intergenic (‑24/+380) | glnH/dps | L‑glutamine ABC transporter periplasmic binding protein/DNA protection during starvation protein |
| * | NC_000913 | 2,412,396 | 0 | C | A | 27.7% | 211.3 / 11.0 | 112 | E67* (GAG→TAG) | yfbU | PF03887 family protein YfbU |
| * | NC_000913 | 2,465,016 | 0 | C | A | 27.7% | 218.2 / 10.3 | 112 | intergenic (‑9/‑285) | mlaA/yfdC | intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA/inner membrane protein YfdC |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2357730 | 112 (1.230) | 10 (0.130) | 9/510 | 5.2 | 9.4% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 95 (1.200) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3648094 | 100 (1.090) | 11 (0.120) +T |
11/588 | 5.3 | 9.6% | noncoding (32/82 nt) | agrA | small RNA AgrA |
| ? | NC_000913 | 3648327 = | 108 (1.180) | noncoding (34/82 nt) | agrB | small regulatory RNA AgrB | |||||
| * | ? | NC_000913 | = 3269899 | 99 (1.080) | 9 (0.100) | 8/554 | 6.0 | 8.7% | intergenic (+297/+317) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 3270239 = | 97 (1.130) | noncoding (354/377 nt) | rnpB | RNase P catalytic RNA component | |||||
| * | ? | NC_000913 | = 1286906 | 45 (0.490) | 9 (0.110) | 7/550 | 6.4 | 16.8% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 47 (0.550) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 696506 | 96 (1.050) | 4 (0.060) | 4/436 | 6.6 | 5.5% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 696619 = | 67 (0.990) | intergenic (‑3/+45) | glnV/metU | tRNA‑Gln/tRNA‑Met | |||||
| * | ? | NC_000913 | = 2653419 | 86 (0.940) | 5 (0.060) | 5/540 | 7.2 | 6.1% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 76 (0.910) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 252776 | 101 (1.110) | 7 (0.080) | 6/590 | 7.2 | 6.5% | coding (68/453 nt) | yafP | putative N‑acetyltransferase YafP |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1287084 | 49 (0.540) | 7 (0.080) | 5/550 | 7.3 | 13.1% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 47 (0.550) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4295870 | 89 (0.970) | 4 (0.050) | 4/512 | 7.5 | 5.5% | intergenic (+76/+566) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296434 = | 59 (0.740) | intergenic (+640/+2) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 781451 | 65 (0.710) | 5 (0.060) | 5/582 | 7.6 | 6.9% | intergenic (+7/‑126) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781660 = | 71 (0.790) | intergenic (+8/‑425) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||