mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,841,246 | 0 | G | T | 30.0% | 44.1 / 16.2 | 40 | A53E (GCG→GAG) | ynjF | CDP‑alcohol phosphatidyltransferase family inner membrane protein |
| * | NC_000913 | 1,197,373 | 0 | A | G | 28.9% | 91.5 / 44.7 | 77 | S54P (TCT→CCT) | ymfD | e14 prophage, putative SAM‑dependent methyltransferase |
| * | NC_000913 | 2,361,533 | 0 | A | T | 20.4% | 82.2 / 12.3 | 46 | I226N (ATC→AAC) | rhmR | putative DNA‑binding transcriptional regulator for the rhm operon |
| * | NC_000913 | 3,913,766 | 0 | C | A | 20.0% | 66.4 / 10.9 | 42 | intergenic (‑99/+63) | glmS/glmU | L‑glutamine:D‑fructose‑6‑phosphate aminotransferase/fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 62 (0.970) | 13 (0.230) | 12/252 | 4.6 | 19.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 54 (0.950) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 53 (0.830) | 13 (0.230) | 11/252 | 4.9 | 20.8% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (0.910) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 381681 = | NA (NA) | 7 (0.120) | 4/266 | 8.8 | NA | coding (331/366 nt) coding (8/906 nt) |
insC1 insD1 |
IS2 repressor TnpA IS2 transposase TnpB |
| ? | NC_000913 | 381753 = | NA (NA) | coding (80/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 4606559 = | NA (NA) | 4 (0.070) | 4/270 | 8.9 | NA | noncoding (1/92 nt) | REP351 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP351 (repetitive extragenic palindromic) element, contains 2 REP sequences |
| ? | NC_000913 | 4606591 = | NA (NA) | noncoding (33/92 nt) | REP351 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP351 (repetitive extragenic palindromic) element, contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2078520 = | 77 (1.200) | 3 (0.050) | 3/264 | 9.4 | 4.0% | intergenic (+413/+29) | yeeW/yoeD | CP4‑44 prophage, uncharacterized protein,Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant,Phage or Prophage Related |
| ? | NC_000913 | 2078552 = | 72 (1.210) | pseudogene (126/129 nt) | yoeD | pseudogene, CP4‑44 putative prophage remnant,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4027517 = | 94 (1.460) | 5 (0.080) | 3/270 | 9.6 | 5.4% | noncoding (197/281 nt) | REP291 (repetitive extragenic palindromic) element, contains 6 REP sequences | REP291 (repetitive extragenic palindromic) element, contains 6 REP sequences |
| ? | NC_000913 | 4027549 = | 87 (1.430) | noncoding (229/281 nt) | REP291 (repetitive extragenic palindromic) element, contains 6 REP sequences | REP291 (repetitive extragenic palindromic) element, contains 6 REP sequences | |||||
| * | ? | NC_000913 | 202024 = | 64 (1.000) | 3 (0.050) | 3/268 | 9.6 | 4.8% | intergenic (+28/‑77) | lpxD/fabZ | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase/(3R)‑hydroxymyristol acyl carrier protein dehydratase |
| ? | NC_000913 | 202060 = | 58 (0.960) | intergenic (+64/‑41) | lpxD/fabZ | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase/(3R)‑hydroxymyristol acyl carrier protein dehydratase | |||||
| * | ? | NC_000913 | 4418517 = | 58 (0.900) | 3 (0.050) | 3/276 | 9.8 | 5.5% | intergenic (‑63/+45) | ulaR/ulaG | transcriptional repressor for the L‑ascorbate utilization divergent operon/L‑ascorbate 6‑phosphate lactonase |
| ? | NC_000913 | 4418549 = | 47 (0.750) | intergenic (‑95/+13) | ulaR/ulaG | transcriptional repressor for the L‑ascorbate utilization divergent operon/L‑ascorbate 6‑phosphate lactonase | |||||
| * | ? | NC_000913 | 3818519 = | 68 (1.060) | 3 (0.050) | 3/278 | 9.8 | 4.4% | coding (761/825 nt) | dinD | DNA damage‑inducible protein |
| ? | NC_000913 | 3818540 = | 63 (1.000) | coding (782/825 nt) | dinD | DNA damage‑inducible protein | |||||
| * | ? | NC_000913 | 285872 = | 62 (0.970) | 3 (0.050) | 3/282 | 9.9 | 4.7% | coding (478/1383 nt) | yagG | CP4‑6 prophage, putative sugar transporter |
| ? | NC_000913 | 285898 = | 59 (0.930) | coding (504/1383 nt) | yagG | CP4‑6 prophage, putative sugar transporter | |||||