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 (highest frequency 20 of 23 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP025268 | 1,292,876 | 0 | C | T | 74.9% | 254.0 / 116.3 | 219 | intergenic (‑18/+29) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,293,160 | 0 | G | A | 71.3% | 129.0 / 56.4 | 105 | noncoding (55/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,292,848 | 0 | A | T | 70.9% | 120.4 / 136.4 | 196 | noncoding (11/132 nt) | CXP41_RS06830 | RtT sRNA |
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 57.9% | 65.6 / 236.2 | 191 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 56.2% | 82.8 / 219.2 | 194 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 4,621,385 | 0 | C | T | 50.1% | 212.6 / inf | 992 | A414V (GCG→GTG) | deoA | thymidine phosphorylase |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 45.4% | 88.6 / 223.6 | 192 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 34.6% | 102.7 / 33.3 | 84 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 2,233,225 | 0 | T | A | 33.8% | 99.4 / 23.4 | 84 | intergenic (+125/+248) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 164,412 | 0 | A | C | 28.6% | 109.9 / 18.1 | 105 | intergenic (+47/‑149) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 28.6% | 138.3 / 57.7 | 107 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 26.6% | 314.2 / 33.3 | 163 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 25.8% | 324.8 / 27.2 | 168 | intergenic (+84/+68) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 2,181,292 | 0 | G | T | 25.7% | 162.8 / 21.9 | 113 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 22.9% | 145.1 / 60.1 | 106 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 22.6% | 324.5 / 118.5 | 234 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 22.2% | 283.9 / 116.8 | 236 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 22.2% | 305.8 / 137.9 | 234 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 2,233,248 | 0 | G | C | 22.1% | 193.3 / 38.2 | 95 | intergenic (+148/+225) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 922,306 | 0 | A | T | 21.7% | 351.9 / 25.3 | 165 | intergenic (‑342/+153) | lysO/aqpZ | L‑lysine exporter LysO/aquaporin Z |
| Marginal new junction evidence (lowest skew 10 of 410 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 695911 = | 1 (0.000) | 205 (0.590) +GAAGAAACAATC |
46/252 | 3.7 | 54.8% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 370 (0.980) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | 1292725 = | 349 (0.920) | 95 (0.300) | 41/234 | 3.8 | 35.1% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 56 (0.170) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 373973 = | 348 (0.920) | 92 (0.240) | 27/276 | 7.6 | 21.3% | intergenic (+41/‑537) | dmpG/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑(3‑hydroxy‑phenyl)propionate transporter |
| ? | NZ_CP025268 | = 374376 | 332 (0.880) | intergenic (+444/‑134) | dmpG/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑(3‑hydroxy‑phenyl)propionate transporter | |||||
| * | ? | NZ_CP025268 | 4544596 = | 21 (0.060) | 52 (0.150) | 24/258 | 7.8 | 54.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | 4544910 = | 69 (0.190) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 4096272 | 279 (0.740) | 24 (0.090) | 14/194 | 8.5 | 9.6% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NZ_CP025268 | 4096641 = | 257 (0.970) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NZ_CP025268 | = 4544604 | 22 (0.060) | 24 (0.070) | 19/258 | 9.1 | 34.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | = 4544900 | 69 (0.190) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 4132088 | 418 (1.100) | 18 (0.050) | 16/252 | 9.9 | 4.5% | coding (332/2433 nt) | metL | bifunctional aspartate kinase/homoserine dehydrogenase II |
| ? | NZ_CP025268 | 4132551 = | 385 (1.110) | coding (795/2433 nt) | metL | bifunctional aspartate kinase/homoserine dehydrogenase II | |||||
| * | ? | NZ_CP025268 | = 684590 | 414 (1.090) | 19 (0.050) | 16/252 | 9.9 | 4.8% | coding (388/675 nt) | gltK | glutamate/aspartate ABC transporter permease GltK |
| ? | NZ_CP025268 | 685289 = | 370 (1.070) | coding (429/741 nt) | gltJ | glutamate/aspartate ABC transporter permease GltJ | |||||
| * | ? | NZ_CP025268 | 780418 = | 238 (0.630) | 80 (0.220) +GAAG |
16/268 | 10.4 | 24.9% | noncoding (1/76 nt) | CXP41_RS04110 | tRNA‑Lys |
| ? | NZ_CP025268 | = 2525041 | 259 (0.680) | noncoding (76/76 nt) | CXP41_RS13255 | tRNA‑Val | |||||
| * | ? | NZ_CP025268 | = 4293125 | 420 (1.110) | 17 (0.050) | 14/250 | 10.6 | 4.5% | coding (727/957 nt) | nrfD | cytochrome c nitrite reductase subunit NrfD |
| ? | NZ_CP025268 | 4294017 = | 340 (0.990) | coding (643/1719 nt) | nrfE | heme lyase CcmF/NrfE family subunit | |||||