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 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP025268 | 1,293,160 | 0 | G | A | 71.8% | 257.5 / 105.5 | 173 | noncoding (55/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 59.6% | 154.5 / inf | 307 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 58.0% | 173.6 / inf | 316 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 51.8% | 27.5 / inf | 324 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 4,621,385 | 0 | C | T | 50.2% | 315.8 / inf | 1404 | A414V (GCG→GTG) | deoA | thymidine phosphorylase |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 30.5% | 202.6 / 37.8 | 131 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 27.5% | 234.0 / 125.8 | 173 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 26.8% | 487.5 / 49.5 | 266 | intergenic (+84/+68) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 26.2% | 293.8 / 92.0 | 174 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 26.0% | 500.2 / 70.7 | 270 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 25.8% | 435.3 / 240.4 | 396 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 2,233,225 | 0 | T | A | 25.6% | 180.8 / 38.2 | 123 | intergenic (+125/+248) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 2,233,248 | 0 | G | C | 25.2% | 291.2 / 61.7 | 147 | intergenic (+148/+225) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 24.7% | 484.6 / 219.6 | 393 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 23.8% | 489.6 / 262.8 | 405 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 3,505,547 | 0 | T | A | 23.6% | 524.4 / 35.1 | 268 | intergenic (+78/+74) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 784,010 | 0 | G | T | 22.7% | 912.4 / 65.5 | 467 | T119T (ACC→ACA) | ybgS | YbgS‑like family protein |
| * | NZ_CP025268 | 623,647 | 0 | A | T | 22.2% | 507.4 / 42.2 | 257 | intergenic (‑88/‑287) | fepB/entC | Fe2+‑enterobactin ABC transporter substrate‑binding protein/isochorismate synthase EntC |
| * | NZ_CP025268 | 4,414,705 | 0 | T | G | 21.9% | 888.5 / 77.3 | 425 | V131V (GTT→GTG) | yjfM | DUF1190 domain‑containing protein |
| * | NZ_CP025268 | 164,412 | 0 | A | C | 21.7% | 205.8 / 21.2 | 166 | intergenic (+47/‑149) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| Marginal new junction evidence (lowest skew 10 of 405 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 1292725 = | 459 (0.830) | 159 (0.340) | 59/232 | 3.0 | 40.4% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 80 (0.170) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | = 1214906 | 657 (1.180) | 100 (0.200) | 61/242 | 3.1 | 16.9% | coding (305/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | = 1216702 | 406 (0.830) | coding (57/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 1214891 = | 665 (1.200) | 120 (0.240) | 55/242 | 3.8 | 19.3% | coding (290/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | 1216719 = | 416 (0.850) | coding (40/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 695911 = | 0 (0.000) | 298 (0.590) +GAAGAAACAATC |
44/250 | 5.6 | 55.8% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 517 (0.930) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | 4544596 = | 21 (0.040) | 92 (0.180) | 38/256 | 6.8 | 60.4% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | 4544910 = | 101 (0.190) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 4096272 | 379 (0.680) | 25 (0.060) | 17/192 | 9.6 | 8.4% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NZ_CP025268 | 4096641 = | 277 (0.710) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NZ_CP025268 | = 3482513 | 377 (0.680) | 25 (0.060) | 18/212 | 10.1 | 7.9% | coding (539/1914 nt) | yheS | ABC transporter ATP‑binding protein |
| ? | NZ_CP025268 | 3483357 = | 293 (0.680) | coding (1383/1914 nt) | yheS | ABC transporter ATP‑binding protein | |||||
| * | ? | NZ_CP025268 | = 4544604 | 31 (0.060) | 30 (0.060) | 23/256 | 10.3 | 31.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | = 4544900 | 99 (0.190) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | 780418 = | 326 (0.590) | 111 (0.210) +GAAG |
21/266 | 11.2 | 23.4% | noncoding (1/76 nt) | CXP41_RS04110 | tRNA‑Lys |
| ? | NZ_CP025268 | = 2525041 | 422 (0.760) | noncoding (76/76 nt) | CXP41_RS13255 | tRNA‑Val | |||||
| * | ? | NZ_CP025268 | = 2821963 | 428 (0.770) | 33 (0.070) | 16/234 | 11.7 | 8.3% | intergenic (‑82/+117) | CXP41_RS14780/CXP41_RS14785 | tRNA‑Arg/tRNA‑Arg |
| ? | NZ_CP025268 | 2822513 = | 360 (0.760) | noncoding (58/77 nt) | CXP41_RS14795 | tRNA‑Arg | |||||