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 229 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 70.0% | 25.9 / 20.2 | 30 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 67.9% | 17.4 / 21.5 | 28 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 579,134 | 0 | T | C | 51.0% | 41.7 / 267.4 | 194 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,302 | 0 | C | T | 51.0% | 24.6 / inf | 206 | R48R (AGG→AGA) | ylcI | DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,120 | 0 | C | T | 50.9% | 1.8 / 266.4 | 175 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,115 | 0 | C | T | 50.9% | ‑6.2 / 256.7 | 175 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,119 | 0 | A | G | 50.6% | 28.0 / 245.8 | 174 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,020 | 0 | G | A | 50.5% | ‑0.2 / 285.3 | 192 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,634,484 | 0 | G | T | 50.5% | 40.6 / 156.3 | 95 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,605 | 0 | T | G | 50.2% | 24.1 / 314.6 | 201 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,127 | 0 | T | C | 50.2% | 29.0 / 283.6 | 199 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,146 | 0 | A | G | 50.0% | 30.3 / 284.5 | 201 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 581,127 | 0 | G | A | 49.6% | 65.5 / 167.1 | 121 | E98E (GAG→GAA) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 1,634,482 | 0 | T | C | 49.5% | 37.7 / 150.2 | 95 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 3,054,886 | 0 | G | T | 49.5% | 54.8 / 62.0 | 93 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 581,118 | 0 | T | C | 48.8% | 54.4 / 187.3 | 126 | D95D (GAT→GAC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 578,729 | 0 | A | G | 48.6% | 12.4 / inf | 218 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,099 | 0 | A | . | 48.4% | 378.7 / inf | 225 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,502 | 0 | A | G | 48.1% | ‑2.3 / inf | 268 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 581,133 | 0 | A | G | 47.9% | 50.5 / 182.0 | 121 | K100K (AAA→AAG) | nohD | putative DNA‑packaging protein NohD |
| 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 | = 4542690 | 105 (1.180) | 26 (0.300) | 21/580 | 2.6 | 19.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 114 (1.320) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 566774 | 71 (0.800) | 27 (0.300) | 15/594 | 3.8 | 25.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 84 (0.950) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4606166 | 95 (1.070) | 7 (0.110) | 7/420 | 4.5 | 9.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 65 (1.040) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 696506 | 0 (0.000) | 9 (0.120) +45 bp |
9/508 | 4.6 | 24.9% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 64 (0.720) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | = 781446 | 44 (0.490) | 6 (0.090) | 6/442 | 5.1 | 14.2% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 40 (0.610) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 3648146 | 122 (1.370) | 6 (0.080) | 6/482 | 5.5 | 5.9% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 93 (1.290) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 696741 | 39 (0.440) | 5 (0.080) | 5/442 | 5.5 | 12.1% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 44 (0.670) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 3469040 | 95 (1.070) | 6 (0.070) | 6/558 | 6.1 | 6.2% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 93 (1.120) | coding (510/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 780629 | 79 (0.890) | 4 (0.060) | 4/446 | 6.1 | 7.0% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 48 (0.720) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | 2818197 = | 29 (0.330) | 4 (0.060) | 3/440 | 6.5 | 11.4% | intergenic (‑62/+1) | argZ/argY | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818471 | 41 (0.620) | intergenic (‑197/+2) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||