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 34 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 | 36.6% | 175.5 / 27.4 | 123 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,427,992 | 0 | G | T | 35.4% | 132.0 / 15.8 | 113 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,073,613 | 0 | G | T | 35.3% | 123.5 / 19.2 | 86 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.5% | 136.1 / 26.8 | 88 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 33.0% | 150.5 / 10.8 | 88 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.2% | 147.1 / 27.0 | 88 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,472,817 | 0 | C | A | 32.0% | 132.2 / 13.2 | 78 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 4,136,467 | 0 | A | C | 31.8% | 105.8 / 18.6 | 63 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 1,334,966 | 0 | A | C | 31.2% | 248.8 / 34.8 | 160 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,767,445 | 0 | C | A | 31.0% | 246.7 / 10.9 | 113 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,922,815 | 0 | C | A | 30.5% | 147.1 / 23.8 | 105 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,288,418 | 0 | G | T | 30.2% | 225.6 / 32.1 | 139 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 2,477,265 | 0 | A | C | 28.6% | 188.6 / 24.2 | 98 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,543,220 | 0 | A | C | 28.4% | 175.9 / 10.0 | 109 | L18F (TTA→TTC) | rpnA | recombination‑promoting nuclease RpnA |
| * | NC_000913 | 2,465,016 | 0 | C | A | 28.1% | 218.5 / 10.7 | 121 | intergenic (‑9/‑285) | mlaA/yfdC | intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA/inner membrane protein YfdC |
| * | NC_000913 | 1,579,973 | 0 | C | A | 27.7% | 267.9 / 14.0 | 137 | G273V (GGA→GTA) | ydeM | putative anaerobic sulfatase maturation enzyme YdeM |
| * | NC_000913 | 4,296,191 | 0 | A | C | 27.3% | 37.2 / 28.6 | 44 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 847,955 | 0 | G | A | 27.2% | 227.4 / 48.5 | 136 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 161,549 | 0 | A | C | 27.2% | 159.2 / 11.4 | 81 | R161R (CGT→CGG) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| * | NC_000913 | 2,457,177 | 0 | T | G | 26.8% | 95.5 / 10.4 | 57 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 17 (0.170) | 15/598 | 5.2 | 13.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 569148 | 110 (1.130) | coding (247/1527 nt) | ybcK | putative recombinase YbcK | |||||
| * | ? | NC_000913 | = 781222 | 50 (0.510) | 11 (0.150) | 8/446 | 5.8 | 21.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 43 (0.590) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 12 (0.120) | 11/598 | 6.3 | 9.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 569145 = | 113 (1.160) | coding (244/1527 nt) | ybcK | putative recombinase YbcK | |||||
| * | ? | NC_000913 | = 3648146 | 118 (1.210) | 7 (0.090) | 7/482 | 6.7 | 7.2% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 85 (1.080) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781322 | 60 (0.610) | 7 (0.080) | 7/520 | 7.1 | 10.4% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 68 (0.800) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4606166 | 101 (1.030) | 5 (0.070) | 4/420 | 7.4 | 7.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 57 (0.830) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781446 | 49 (0.500) | 3 (0.040) | 3/442 | 8.3 | 7.0% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 43 (0.600) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 184226 = | 99 (1.020) | 5 (0.050) | 5/596 | 8.8 | 4.8% | intergenic (‑131/+31) | yaeH/yaeI | DUF3461 domain‑containing protein YaeH/phosphodiesterase YaeI |
| ? | NC_000913 | 270541 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 4606286 | 75 (0.770) | 3 (0.040) | 3/504 | 9.1 | 4.0% | noncoding (1/87 nt) | leuP | tRNA‑Leu |
| ? | NC_000913 | 4606402 = | 79 (0.960) | intergenic (‑1/+267) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2653390 | 88 (0.900) | 5 (0.050) +A |
4/596 | 9.4 | 5.4% | noncoding (66/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653718 = | 87 (0.890) | intergenic (‑263/‑137) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||