mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 64.4% | 248.1 / inf | 341 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 61.5% | 256.9 / inf | 367 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 55.1% | 32.6 / inf | 375 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 34.7% | 304.0 / 67.1 | 200 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 164,438 | 0 | T | A | 25.4% | 308.3 / 21.8 | 152 | intergenic (+73/‑123) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 2,233,248 | 0 | G | C | 25.2% | 444.0 / 108.1 | 215 | intergenic (+148/+225) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 24.9% | 481.5 / 293.5 | 445 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 24.9% | 473.4 / 293.3 | 458 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 23.9% | 551.1 / 259.1 | 457 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 3,505,547 | 0 | T | A | 23.3% | 716.6 / 43.6 | 343 | intergenic (+78/+74) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 164,395 | 0 | A | T | 23.3% | 426.8 / 20.8 | 218 | intergenic (+30/‑166) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 22.6% | 321.4 / 118.5 | 207 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 22.1% | 668.0 / 43.2 | 336 | intergenic (+84/+68) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 2,233,225 | 0 | T | A | 22.1% | 321.0 / 40.9 | 198 | intergenic (+125/+248) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 164,444 | 0 | T | A | 22.0% | 343.5 / 15.3 | 145 | intergenic (+79/‑117) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 2,233,226 | 0 | C | A | 21.9% | 333.7 / 22.6 | 187 | intergenic (+126/+247) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 2,181,292 | 0 | G | T | 21.6% | 319.8 / 45.3 | 194 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 21.5% | 381.0 / 88.1 | 206 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 21.4% | 697.5 / 47.5 | 330 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 164,426 | 0 | T | G | 20.8% | 349.7 / 17.4 | 154 | intergenic (+61/‑135) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| Marginal new junction evidence (lowest skew 10 of 478 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 1292725 = | 572 (0.900) | 200 (0.370) | 62/232 | 3.7 | 40.9% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 93 (0.170) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 1214891 = | 680 (1.060) | 127 (0.230) | 62/242 | 4.0 | 20.0% | coding (290/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | 1216719 = | 416 (0.740) | coding (40/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 66565 = | 257 (0.400) | 151 (0.340) +43 bp |
47/188 | 4.0 | 45.5% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 66606 | 271 (0.420) | intergenic (‑55/+60) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase | |||||
| * | ? | NZ_CP025268 | 66565 = | 258 (0.400) | 163 (0.340) +35 bp |
51/204 | 4.1 | 45.2% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 66614 | 273 (0.430) | intergenic (‑63/+52) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase | |||||
| * | ? | NZ_CP025268 | = 1214906 | 653 (1.020) | 100 (0.180) | 56/242 | 4.8 | 16.9% | coding (305/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | = 1216702 | 410 (0.730) | coding (57/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 695911 = | 0 (0.000) | 314 (0.540) +GAAGAAACAATC |
50/250 | 5.9 | 56.2% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 537 (0.840) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | 66565 = | 258 (0.400) | 155 (0.250) +TTCAAC |
40/262 | 8.1 | 26.6% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 2435047 | 635 (0.990) | intergenic (‑249/+10) | cvpA/dedD | colicin V production protein/cell division protein DedD | |||||
| * | ? | NZ_CP025268 | 66565 = | 258 (0.400) | 150 (0.250) +TTCAAC |
38/262 | 8.5 | 23.4% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | 4029440 = | 770 (1.200) | intergenic (+290/+91) | fre/fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA | |||||
| * | ? | NZ_CP025268 | 66565 = | 258 (0.400) | 150 (0.250) +TTCAAC |
38/262 | 8.5 | 24.1% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | 3044744 = | 732 (1.150) | intergenic (+147/+49) | ygfZ/yqfA | tRNA‑modifying protein YgfZ/hemolysin III family protein | |||||
| * | ? | NZ_CP025268 | 66565 = | 258 (0.400) | 150 (0.250) +TTCAAC |
38/262 | 8.5 | 26.8% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 2351362 | 598 (0.940) | intergenic (+177/+23) | nrdA/CXP41_RS24490 | ribonucleoside‑diphosphate reductase subunit alpha/protein YoaM | |||||