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 | 339,986 | 0 | G | A | 73.5% | 36.5 / 20.8 | 34 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 72.7% | 29.4 / 24.0 | 33 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 375,067 | 0 | A | G | 56.2% | 12.8 / 33.2 | 32 | intergenic (+186/‑392) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 375,075 | 0 | G | A | 50.0% | ‑0.6 / 37.1 | 34 | intergenic (+194/‑384) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 2,995,560 | 0 | C | A | 40.3% | 144.3 / 193.6 | 154 | intergenic (+1704/+812) | ygeI/insD4 | protein YgeI/IS2 insertion element protein InsB |
| * | NC_000913 | 2,767,444 | 0 | C | A | 39.8% | 191.9 / 17.8 | 119 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,243,809 | 0 | C | A | 38.1% | 100.9 / 105.1 | 98 | L311L (CTG→CTT) | uxaC | D‑glucoronate/D‑galacturonate isomerase |
| * | NC_000913 | 2,767,445 | 0 | C | A | 37.3% | 168.5 / 38.1 | 119 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,443 | 0 | C | A | 36.4% | 202.7 / 17.0 | 118 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,054,894 | 0 | G | T | 36.0% | 116.7 / 30.8 | 89 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 738,514 | 0 | A | G | 35.7% | 217.2 / 261.8 | 227 | G141G (GGA→GGG) | ybfD | H repeat‑associated putative transposase YbfD |
| * | NC_000913 | 832,448 | 0 | G | A | 34.7% | 105.5 / 21.3 | 75 | intergenic (+212/+20) | rhlE/ybiA | ATP‑dependent RNA helicase RhlE/N‑glycosidase YbiA |
| * | NC_000913 | 2,767,449 | 0 | C | A | 34.2% | 227.6 / 16.7 | 125 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,447 | 0 | C | A | 33.1% | 228.1 / 18.1 | 125 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,334,966 | 0 | A | C | 33.0% | 248.7 / 40.2 | 188 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,477,265 | 0 | A | C | 32.5% | 151.7 / 27.1 | 83 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.3% | 153.3 / 29.8 | 93 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,425,418 | 0 | C | A | 31.8% | 320.2 / 26.7 | 189 | P101T (CCG→ACG) | rpsF | 30S ribosomal subunit protein S6 |
| * | NC_000913 | 1,427,992 | 0 | G | T | 30.3% | 183.8 / 10.2 | 110 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,543,220 | 0 | A | C | 29.2% | 259.4 / 17.6 | 144 | L18F (TTA→TTC) | rpnA | recombination‑promoting nuclease RpnA |
| Marginal new junction evidence (lowest skew 10 of 49 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 270541 = | NA (NA) | 40 (0.340) | 28/598 | 3.5 | 48.2% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1910138 | 43 (0.370) | intergenic (‑39/‑138) | kdgR/yebQ | DNA‑binding transcriptional repressor KdgR/putative transporter YebQ | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 26 (0.220) | 22/598 | 4.6 | 20.0% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1995729 = | 104 (0.900) | coding (75/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | 4542682 = | 150 (1.290) | 19 (0.170) | 19/580 | 5.1 | 12.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 122 (1.080) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 159 (1.370) | 18 (0.160) | 17/580 | 5.6 | 11.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 121 (1.080) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 23 (0.200) | 17/594 | 5.7 | 18.4% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1995730 | 102 (0.890) | coding (76/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 18 (0.160) | 15/592 | 6.2 | 29.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1910136 = | 44 (0.380) | intergenic (‑37/‑140) | kdgR/yebQ | DNA‑binding transcriptional repressor KdgR/putative transporter YebQ | |||||
| * | ? | NC_000913 | = 280111 | NA (NA) | 15 (0.130) | 14/598 | 6.6 | 12.6% | noncoding (181/181 nt) | IS30 | repeat region |
| ? | NC_000913 | 1995729 = | 104 (0.900) | coding (75/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 14 (0.120) | 13/594 | 6.9 | 11.9% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1995729 = | 104 (0.900) | coding (75/177 nt) | yecU | protein YecU | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 11 (0.090) | 9/598 | 8.4 | 10.1% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2732321 = | 98 (0.840) | coding (1409/2130 nt) coding (1853/2574 nt) |
clpB clpB |
chaperone protein ClpB chaperone protein ClpB |
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| * | ? | NC_000913 | = 602863 | 107 (0.920) | 10 (0.090) | 9/598 | 8.4 | 8.5% | coding (905/1377 nt) | pheP | phenylalanine:H(+) symporter PheP |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||