mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 46.9% | 3.5 / 39.9 | 32 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 963,761 | 0 | T | C | 30.0% | 37.5 / 20.0 | 30 | intergenic (+93/‑67) | rpsA/ihfB | 30S ribosomal subunit protein S1/integration host factor (IHF), DNA‑binding protein, beta subunit |
| * | NC_000913 | 963,762 | 0 | A | G | 30.0% | 38.1 / 19.7 | 30 | intergenic (+94/‑66) | rpsA/ihfB | 30S ribosomal subunit protein S1/integration host factor (IHF), DNA‑binding protein, beta subunit |
| * | NC_000913 | 963,763 | 0 | C | T | 30.0% | 38.3 / 20.1 | 30 | intergenic (+95/‑65) | rpsA/ihfB | 30S ribosomal subunit protein S1/integration host factor (IHF), DNA‑binding protein, beta subunit |
| * | NC_000913 | 963,764 | 0 | G | A | 28.1% | 43.5 / 19.4 | 32 | intergenic (+96/‑64) | rpsA/ihfB | 30S ribosomal subunit protein S1/integration host factor (IHF), DNA‑binding protein, beta subunit |
| * | NC_000913 | 2,596,873 | 0 | C | . | 26.1% | 54.0 / 17.6 | 23 | intergenic (‑136/+32) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| * | NC_000913 | 1,015,206 | 0 | T | C | 23.1% | 43.1 / 10.6 | 26 | V104A (GTT→GCT) ‡ | pqiC | DUF330 family putative lipoprotein |
| * | NC_000913 | 1,015,207 | 0 | T | A | 23.1% | 45.6 / 11.7 | 26 | V104V (GTT→GTA) ‡ | pqiC | DUF330 family putative lipoprotein |
| * | NC_000913 | 1,015,203 | 0 | T | A | 22.2% | 46.8 / 11.6 | 27 | V103E (GTG→GAG) | pqiC | DUF330 family putative lipoprotein |
| * | NC_000913 | 2,596,878 | 1 | . | G | 22.2% | 66.5 / 25.3 | 27 | intergenic (‑141/+27) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| * | NC_000913 | 3,140,352 | 0 | G | C | 21.9% | 71.7 / 15.2 | 32 | R150G (CGC→GGC) | hybE | hydrogenase 2‑specific chaperone |
| * | NC_000913 | 574,486 | 1 | . | C | 20.8% | 60.3 / 19.8 | 24 | intergenic (+147/+43) | quuD/nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| * | NC_000913 | 3,234,708 | 0 | T | A | 20.7% | 51.0 / 11.7 | 29 | intergenic (‑253/+31) | higB/rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,234,709 | 0 | T | A | 20.7% | 55.6 / 11.7 | 29 | intergenic (‑254/+30) | higB/rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,368,220 | 0 | C | G | 20.7% | 64.3 / 13.7 | 30 | L132V (CTG→GTG) ‡ | yhcG | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| * | NC_000913 | 3,234,715 | 0 | G | T | 20.0% | 64.8 / 10.4 | 30 | intergenic (‑260/+24) | higB/rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,234,716 | 0 | C | T | 20.0% | 59.7 / 10.1 | 30 | intergenic (‑261/+23) | higB/rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,368,221 | 0 | T | C | 20.0% | 59.6 / 10.4 | 30 | L132P (CTG→CCG) ‡ | yhcG | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| Marginal new junction evidence (lowest skew 10 of 139 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 56 (1.510) | 12 (0.350) | 12/218 | 1.8 | 16.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 66 (1.930) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4542682 = | 56 (1.510) | 10 (0.290) | 8/218 | 2.6 | 14.5% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 66 (1.930) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 238140 | 73 (1.970) | 8 (0.230) | 8/218 | 2.6 | 10.3% | intergenic (+20/+117) | yafT/ykfM | lipoprotein/lethality reduction protein, putative inner membrane protein |
| ? | NC_000913 | = 238146 | 72 (2.110) | intergenic (+26/+111) | yafT/ykfM | lipoprotein/lethality reduction protein, putative inner membrane protein | |||||
| * | ? | NC_000913 | 179793 = | 49 (1.320) | 7 (0.200) | 7/224 | 3.0 | 13.7% | coding (557/1518 nt) | dgt | deoxyguanosine triphosphate triphosphohydrolase |
| ? | NC_000913 | 179819 = | 42 (1.200) | coding (583/1518 nt) | dgt | deoxyguanosine triphosphate triphosphohydrolase | |||||
| * | ? | NC_000913 | = 953472 | 50 (1.350) | 6 (0.180) | 6/218 | 3.2 | 12.2% | coding (83/2283 nt) | pflB | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| ? | NC_000913 | = 953483 | 40 (1.170) | coding (72/2283 nt) | pflB | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 6 (0.180) | 6/216 | 3.2 | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 281896 = | 70 (1.890) | 6 (0.170) | 6/220 | 3.2 | 8.3% | coding (88/1155 nt) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | 281923 = | 67 (1.940) | coding (61/1155 nt) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 8 (0.230) | 6/218 | 3.2 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 225915 | NA (NA) | 6 (0.170) | 6/220 | 3.2 | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225926 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 4007358 | 28 (0.760) | 6 (0.170) | 6/222 | 3.3 | 17.8% | coding (1495/1830 nt) | recQ | ATP‑dependent DNA helicase |
| ? | NC_000913 | = 4007368 | 29 (0.830) | coding (1505/1830 nt) | recQ | ATP‑dependent DNA helicase | |||||