mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,911,533 | 0 | C | A | 37.8% | 175.7 / 21.9 | 119 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,296,191 | 0 | A | C | 36.8% | 6.4 / 12.4 | 19 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 58,065 | 0 | C | A | 34.3% | 173.7 / 18.5 | 108 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,669,715 | 0 | G | T | 33.9% | 159.7 / 16.7 | 109 | E42* (GAG→TAG) | treF | cytoplasmic trehalase |
| * | NC_000913 | 1,427,992 | 0 | G | T | 33.6% | 219.4 / 15.9 | 143 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,722,838 | 0 | G | T | 33.3% | 184.4 / 12.0 | 114 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 4,074,572 | 0 | C | A | 33.0% | 197.5 / 12.3 | 109 | P278P (CCC→CCA) | yihV | 6‑deoxy‑6‑sulfofructose kinase |
| * | NC_000913 | 1,502,770 | 0 | T | C | 31.8% | 149.0 / 33.2 | 110 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 4,296,190 | 0 | A | G | 31.6% | 15.5 / 11.2 | 19 | intergenic (+396/+246) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,001,094 | 0 | G | T | 30.1% | 226.3 / 17.1 | 134 | E627* (GAG→TAG) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 458,024 | 0 | G | T | 29.5% | 204.7 / 11.2 | 105 | R200L (CGA→CTA) | clpX | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| * | NC_000913 | 1,097,118 | 0 | C | A | 28.9% | 40.4 / 24.1 | 38 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 952,453 | 0 | G | T | 28.7% | 259.6 / 21.0 | 143 | P368T (CCG→ACG) | pflB | pyruvate formate‑lyase |
| * | NC_000913 | 3,623,537 | 0 | G | A | 28.5% | 243.7 / 32.1 | 155 | G47S (GGT→AGT) | yhhH | PF15631 family protein YhhH |
| * | NC_000913 | 2,288,418 | 0 | G | T | 28.2% | 284.2 / 14.9 | 142 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 12,152 | 0 | G | T | 28.1% | 259.7 / 10.3 | 135 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 1,922,815 | 0 | C | A | 28.1% | 263.6 / 18.6 | 139 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,477,265 | 0 | A | C | 28.0% | 180.1 / 18.1 | 93 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,269,981 | 0 | A | C | 27.7% | 149.7 / 12.6 | 84 | intergenic (+379/+235) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 847,955 | 0 | G | A | 27.7% | 212.8 / 53.8 | 144 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| Marginal new junction evidence (lowest skew 10 of 44 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 97 (0.930) | 8 (0.110) | 8/406 | 5.0 | 10.4% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 71 (0.980) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3648146 | 114 (1.090) | 11 (0.130) | 9/468 | 5.4 | 10.0% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 106 (1.270) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2653419 | 94 (0.900) | 10 (0.100) | 10/534 | 5.7 | 10.9% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 77 (0.810) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2518116 | 76 (0.730) | 6 (0.080) | 6/422 | 6.0 | 10.7% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 45 (0.600) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 2357730 | 127 (1.220) | 8 (0.090) | 8/504 | 6.1 | 6.9% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 106 (1.180) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4542690 | 125 (1.200) | 12 (0.120) | 9/566 | 6.3 | 9.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 111 (1.100) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2357690 | 140 (1.340) | 8 (0.080) | 8/534 | 6.4 | 6.1% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 117 (1.230) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3469040 | 112 (1.070) | 8 (0.080) | 8/544 | 6.5 | 7.0% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 107 (1.100) | coding (510/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | 781369 = | 62 (0.590) | 10 (0.100) +G |
8/582 | 6.8 | 15.9% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521127 | 44 (0.420) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | 781369 = | 62 (0.590) | 10 (0.100) +GG |
8/580 | 6.8 | 11.9% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 87 (0.830) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||