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 25 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 | 71.8% | 411.0 / 247.4 | 396 | intergenic (‑18/+29) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,848 | 0 | A | T | 71.8% | 225.4 / 236.9 | 342 | noncoding (11/132 nt) | CXP41_RS06830 | RtT sRNA |
| * | NZ_CP025268 | 1,293,160 | 0 | G | A | 68.4% | 170.6 / 92.9 | 140 | noncoding (55/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 67.9% | 251.4 / 239.3 | 277 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 63.1% | 215.1 / 262.6 | 294 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 58.8% | 60.1 / inf | 302 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 2,175,464 | 0 | A | T | 49.4% | 45.4 / inf | 439 | intergenic (+27/+3) | CXP41_RS11550/CXP41_RS11555 | IS3‑like element IS3 family transposase/DeoR family transcriptional regulator |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 32.7% | 244.4 / 50.6 | 161 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 30.9% | 201.2 / 86.8 | 147 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 29.3% | 181.4 / 111.8 | 147 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 2,233,225 | 0 | T | A | 29.0% | 221.1 / 37.2 | 149 | intergenic (+125/+248) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 28.0% | 445.1 / 52.0 | 246 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 27.3% | 450.5 / 261.1 | 407 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 27.3% | 411.9 / 316.6 | 407 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 26.7% | 387.8 / 316.0 | 408 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 164,412 | 0 | A | C | 26.1% | 208.3 / 15.3 | 161 | intergenic (+47/‑149) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 2,233,248 | 0 | G | C | 25.1% | 344.0 / 72.9 | 176 | intergenic (+148/+225) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 24.0% | 546.4 / 62.2 | 266 | intergenic (+84/+68) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 623,647 | 0 | A | T | 23.9% | 443.9 / 41.7 | 242 | intergenic (‑88/‑287) | fepB/entC | Fe2+‑enterobactin ABC transporter substrate‑binding protein/isochorismate synthase EntC |
| * | NZ_CP025268 | 3,505,561 | 0 | T | A | 22.4% | 507.9 / 52.5 | 246 | intergenic (+92/+60) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| Marginal new junction evidence (lowest skew 10 of 311 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 1292725 = | 537 (0.930) | 169 (0.350) | 55/232 | 3.3 | 39.0% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 74 (0.150) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 695911 = | 0 (0.000) | 298 (0.570) +GAAGAAACAATC |
50/250 | 4.4 | 56.6% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 502 (0.870) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | 4544596 = | 22 (0.040) | 64 (0.120) | 32/256 | 7.5 | 48.6% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | 4544910 = | 115 (0.210) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 780371 | 404 (0.700) | 27 (0.070) | 21/196 | 8.0 | 10.5% | intergenic (+100/‑47) | CXP41_RS04105/CXP41_RS04110 | tRNA‑Lys/tRNA‑Lys |
| ? | NZ_CP025268 | 780860 = | 170 (0.410) | intergenic (+3/‑274) | CXP41_RS04120/nadA | RtT sRNA/quinolinate synthase NadA | |||||
| * | ? | NZ_CP025268 | = 4096272 | 416 (0.720) | 20 (0.050) | 17/192 | 9.0 | 5.6% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NZ_CP025268 | 4096641 = | 388 (0.970) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NZ_CP025268 | 2769444 = | 712 (1.240) | 16 (0.040) | 14/186 | 9.8 | 3.3% | intergenic (‑267/+93) | abpA/yfjM | anti‑bacteriophage protein AbpA/DUF1524 domain‑containing protein |
| ? | NZ_CP025268 | = 2769435 | 465 (1.200) | intergenic (‑258/+102) | abpA/yfjM | anti‑bacteriophage protein AbpA/DUF1524 domain‑containing protein | |||||
| * | ? | NZ_CP025268 | = 1292745 | 435 (0.760) | 21 (0.040) | 19/232 | 10.0 | 8.7% | noncoding (114/132 nt) | CXP41_RS06830 | RtT sRNA |
| ? | NZ_CP025268 | 1293280 = | 74 (0.150) | noncoding (66/85 nt) | CXP41_RS06845 | tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 932964 = | 444 (0.770) | 45 (0.120) | 13/182 | 10.0 | 16.3% | intergenic (+317/+27) | clpA/CXP41_RS04925 | ATP‑dependent Clp protease ATP‑binding subunit ClpA/tRNA‑Ser |
| ? | NZ_CP025268 | = 1104277 | 169 (0.440) | intergenic (+346/+28) | CXP41_RS05715/CXP41_RS05720 | protein YcdU/RtT sRNA | |||||
| * | ? | NZ_CP025268 | = 780065 | 405 (0.700) | 23 (0.050) | 15/200 | 10.1 | 9.0% | intergenic (+98/‑52) | CXP41_RS04095/CXP41_RS04100 | tRNA‑Lys/tRNA‑Val |
| ? | NZ_CP025268 | 780858 = | 172 (0.410) | intergenic (+1/‑276) | CXP41_RS04120/nadA | RtT sRNA/quinolinate synthase NadA | |||||
| * | ? | NZ_CP025268 | = 1292745 | 435 (0.760) | 20 (0.040) | 18/234 | 10.4 | 5.4% | noncoding (114/132 nt) | CXP41_RS06830 | RtT sRNA |
| ? | NZ_CP025268 | 1293574 = | 323 (0.660) | noncoding (66/85 nt) | CXP41_RS06855 | tRNA‑Tyr | |||||