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 | 1,292,848 | 0 | A | T | 72.3% | 229.1 / 193.0 | 304 | noncoding (11/132 nt) | CXP41_RS06830 | RtT sRNA |
| * | NZ_CP025268 | 1,293,160 | 0 | G | A | 72.0% | 182.8 / 74.5 | 136 | noncoding (55/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 63.5% | 148.4 / 259.7 | 255 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 63.3% | 185.5 / 245.5 | 274 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 53.0% | 35.6 / inf | 272 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 4,621,385 | 0 | C | T | 48.9% | 174.5 / inf | 1506 | A414V (GCG→GTG) | deoA | thymidine phosphorylase |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 30.1% | 150.3 / 108.4 | 138 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 2,474,470 | 0 | C | A | 29.9% | 123.6 / 11.7 | 87 | Q436K (CAA→AAA) | CXP41_RS13000 | hypothetical protein |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 29.8% | 184.6 / 85.6 | 139 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 2,474,461 | 0 | C | A | 29.3% | 87.5 / 16.6 | 82 | Q433K (CAA→AAA) | CXP41_RS13000 | hypothetical protein |
| * | NZ_CP025268 | 164,412 | 0 | A | C | 29.2% | 169.7 / 19.9 | 130 | intergenic (+47/‑149) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 24.3% | 439.8 / 208.3 | 385 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 23.8% | 476.0 / 39.4 | 240 | intergenic (+84/+68) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 922,306 | 0 | A | T | 23.4% | 556.6 / 70.5 | 290 | intergenic (‑342/+153) | lysO/aqpZ | L‑lysine exporter LysO/aquaporin Z |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 23.3% | 315.4 / 41.3 | 167 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 23.0% | 519.1 / 200.1 | 378 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 22.4% | 485.2 / 223.5 | 375 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 164,395 | 0 | A | T | 21.9% | 281.3 / 17.2 | 145 | intergenic (+30/‑166) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 21.4% | 462.6 / 48.7 | 234 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 2,233,248 | 0 | G | C | 20.9% | 419.4 / 57.7 | 182 | intergenic (+148/+225) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| Marginal new junction evidence (lowest skew 10 of 510 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 1214891 = | 602 (1.070) | 114 (0.230) | 67/244 | 2.4 | 19.4% | coding (290/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | 1216719 = | 414 (0.830) | coding (40/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 66565 = | 223 (0.400) | 135 (0.320) +35 bp |
50/206 | 3.0 | 44.0% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 66614 | 237 (0.420) | intergenic (‑63/+52) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase | |||||
| * | ? | NZ_CP025268 | 1292725 = | 486 (0.860) | 143 (0.300) | 55/234 | 3.3 | 36.6% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 84 (0.180) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 695911 = | 0 (0.000) | 276 (0.540) +GAAGAAACAATC |
52/252 | 4.1 | 54.0% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 515 (0.910) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | 4544596 = | 63 (0.110) | 84 (0.160) | 42/258 | 5.7 | 49.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | 4544910 = | 116 (0.220) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 4544604 | 51 (0.090) | 78 (0.150) | 38/258 | 6.4 | 49.1% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | = 4544900 | 114 (0.220) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | = 3482513 | 420 (0.750) | 29 (0.070) | 23/214 | 8.1 | 8.2% | coding (539/1914 nt) | yheS | ABC transporter ATP‑binding protein |
| ? | NZ_CP025268 | 3483357 = | 325 (0.740) | coding (1383/1914 nt) | yheS | ABC transporter ATP‑binding protein | |||||
| * | ? | NZ_CP025268 | = 780371 | 417 (0.740) | 26 (0.060) | 20/198 | 8.3 | 9.8% | intergenic (+100/‑47) | CXP41_RS04105/CXP41_RS04110 | tRNA‑Lys/tRNA‑Lys |
| ? | NZ_CP025268 | 780860 = | 180 (0.450) | intergenic (+3/‑274) | CXP41_RS04120/nadA | RtT sRNA/quinolinate synthase NadA | |||||
| * | ? | NZ_CP025268 | = 4293125 | 646 (1.150) | 25 (0.050) | 22/250 | 9.6 | 4.4% | coding (727/957 nt) | nrfD | cytochrome c nitrite reductase subunit NrfD |
| ? | NZ_CP025268 | 4294017 = | 501 (0.980) | coding (643/1719 nt) | nrfE | heme lyase CcmF/NrfE family subunit | |||||
| * | ? | NZ_CP025268 | = 684590 | 705 (1.250) | 27 (0.050) | 22/252 | 9.7 | 4.2% | coding (388/675 nt) | gltK | glutamate/aspartate ABC transporter permease GltK |
| ? | NZ_CP025268 | 685289 = | 590 (1.150) | coding (429/741 nt) | gltJ | glutamate/aspartate ABC transporter permease GltJ | |||||