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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP025268 | 1,292,876 | 0 | C | T | 74.4% | 541.6 / 259.2 | 469 | intergenic (‑18/+29) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,848 | 0 | A | T | 72.1% | 297.8 / 284.7 | 432 | noncoding (11/132 nt) | CXP41_RS06830 | RtT sRNA |
| * | NZ_CP025268 | 1,293,160 | 0 | G | A | 71.4% | 261.9 / 116.8 | 190 | noncoding (55/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,293,000 | 0 | A | G | 65.3% | 252.6 / 287.3 | 299 | noncoding (37/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,991 | 0 | C | T | 60.2% | 241.6 / inf | 324 | noncoding (46/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 1,292,982 | 0 | A | G | 52.1% | 7.6 / inf | 328 | noncoding (55/132 nt) | CXP41_RS06835 | RtT sRNA |
| * | NZ_CP025268 | 4,621,385 | 0 | C | T | 49.7% | 284.3 / inf | 1575 | A414V (GCG→GTG) | deoA | thymidine phosphorylase |
| * | NZ_CP025268 | 2,233,239 | 0 | T | A | 30.7% | 282.3 / 55.7 | 174 | intergenic (+139/+234) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 3,505,559 | 0 | T | A | 27.1% | 536.5 / 75.0 | 294 | intergenic (+90/+62) | phoB/yhfS | DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| * | NZ_CP025268 | 164,395 | 0 | A | T | 26.7% | 337.3 / 38.2 | 201 | intergenic (+30/‑166) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 1,293,169 | 0 | C | T | 25.0% | 264.7 / 126.8 | 194 | noncoding (46/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,292,891 | 0 | G | A | 24.4% | 585.7 / inf | 492 | intergenic (‑33/+14) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 164,412 | 0 | A | C | 24.2% | 251.5 / 25.4 | 194 | intergenic (+47/‑149) | hrpB/mrcB | ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase |
| * | NZ_CP025268 | 1,293,178 | 0 | A | G | 24.2% | 312.5 / 100.2 | 196 | noncoding (37/132 nt) | CXP41_RS06840 | RtT sRNA |
| * | NZ_CP025268 | 1,292,883 | 0 | A | G | 24.0% | 632.6 / 274.8 | 495 | intergenic (‑25/+22) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 1,292,887 | 0 | C | A | 23.7% | 567.9 / 313.2 | 497 | intergenic (‑29/+18) | CXP41_RS06830/CXP41_RS06835 | RtT sRNA/RtT sRNA |
| * | NZ_CP025268 | 3,505,553 | 0 | T | A | 22.7% | 596.2 / 46.4 | 309 | 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 | 22.4% | 302.3 / 16.6 | 172 | intergenic (+125/+248) | yohP/dusC | small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC |
| * | NZ_CP025268 | 3,609,390 | 0 | A | T | 21.6% | 901.1 / 68.3 | 403 | intergenic (+54/+48) | zntA/tusA | Zn(II)/Cd(II)/Pb(II) translocating P‑type ATPase ZntA/sulfurtransferase TusA |
| * | NZ_CP025268 | 107,386 | 0 | A | T | 21.6% | 784.9 / 61.8 | 353 | intergenic (+81/‑150) | lpxC/secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/secA translation cis‑regulator SecM |
| Marginal new junction evidence (lowest skew 10 of 499 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP025268 | 1292725 = | 615 (0.920) | 213 (0.380) | 59/232 | 3.3 | 41.6% | intergenic (+182/+2) | narI/CXP41_RS06830 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| ? | NZ_CP025268 | = 1293258 | 77 (0.140) | intergenic (‑44/+3) | CXP41_RS06840/CXP41_RS06845 | RtT sRNA/tRNA‑Tyr | |||||
| * | ? | NZ_CP025268 | 66565 = | 229 (0.340) | 201 (0.440) +43 bp |
47/188 | 3.3 | 55.7% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 66606 | 238 (0.360) | intergenic (‑55/+60) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase | |||||
| * | ? | NZ_CP025268 | 1214891 = | 803 (1.200) | 114 (0.190) | 61/242 | 3.4 | 16.0% | coding (290/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | 1216719 = | 493 (0.830) | coding (40/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 695911 = | 0 (0.000) | 319 (0.520) +GAAGAAACAATC |
51/250 | 4.8 | 55.0% | intergenic (‑33/+2) | CXP41_RS03680/CXP41_RS03685 | tRNA‑Gln/tRNA‑Gln |
| ? | NZ_CP025268 | = 696182 | 573 (0.860) | intergenic (‑1/+379) | CXP41_RS03695/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP025268 | = 1214906 | 781 (1.170) | 79 (0.130) | 46/242 | 5.3 | 11.8% | coding (305/630 nt) | CXP41_RS06370 | protein StfP |
| ? | NZ_CP025268 | = 1216702 | 488 (0.830) | coding (57/540 nt) | CXP41_RS06385 | phage tail protein | |||||
| * | ? | NZ_CP025268 | 4544596 = | 23 (0.030) | 87 (0.140) | 42/256 | 6.3 | 55.9% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP025268 | 4544910 = | 116 (0.190) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP025268 | 66565 = | 229 (0.340) | 166 (0.260) +TTCAAC |
42/262 | 6.5 | 28.0% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | = 2435047 | 663 (0.990) | intergenic (‑249/+10) | cvpA/dedD | colicin V production protein/cell division protein DedD | |||||
| * | ? | NZ_CP025268 | 66565 = | 229 (0.340) | 154 (0.230) +T |
42/272 | 6.8 | 26.4% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | 215927 = | 636 (0.950) | intergenic (+118/+82) | nlpE/yaeF | envelope stress response activation lipoprotein NlpE/YaeF family permuted papain‑like enzyme | |||||
| * | ? | NZ_CP025268 | 66565 = | 229 (0.340) | 155 (0.240) +TTCAAC |
40/262 | 6.9 | 24.9% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | 4029440 = | 749 (1.120) | intergenic (+290/+91) | fre/fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA | |||||
| * | ? | NZ_CP025268 | 66565 = | 229 (0.340) | 155 (0.240) +TTCAAC |
40/262 | 6.9 | 23.6% | intergenic (‑14/+101) | araD/araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| ? | NZ_CP025268 | 3044744 = | 820 (1.220) | intergenic (+147/+49) | ygfZ/yqfA | tRNA‑modifying protein YgfZ/hemolysin III family protein | |||||