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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 28.9% | 191.0 / 84.2 | 114 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 28.8% | 232.2 / 117.9 | 118 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,792 | 0 | A | C | 28.6% | 175.8 / 107.9 | 119 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 23.5% | 206.1 / 62.1 | 115 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_pgi | 1,018,986 | 0 | A | T | 20.9% | 297.3 / 79.5 | 130 | intergenic (+49/+27) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| * | NC_000913_3_pae_pgi | 1,018,983 | 0 | A | T | 20.8% | 304.1 / 75.0 | 130 | intergenic (+46/+30) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| * | NC_000913_3_pae_pgi | 53,376 | 0 | G | A | 20.2% | 270.8 / 66.0 | 130 | P14L (CCC→CTC) | pdxA | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| Marginal new junction evidence (lowest skew 10 of 665 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 1018982 | 125 (1.290) | 29 (0.330) | 21/238 | 6.0 | 20.1% | intergenic (+45/+31) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| ? | NC_000913_3_pae_pgi | = 1018986 | 117 (1.320) | intergenic (+49/+27) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) | |||||
| * | ? | NC_000913_3_pae_pgi | = 2079003 | 112 (1.160) | 20 (0.230) | 19/232 | 6.4 | 17.2% | intergenic (+72/+29) | yoeF/yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein |
| ? | NC_000913_3_pae_pgi | = 2079004 | 92 (1.070) | intergenic (+73/+28) | yoeF/yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 382211 | NA (NA) | 28 (0.300) | 21/250 | 6.4 | NA | coding (538/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913_3_pae_pgi | = 382218 | NA (NA) | coding (545/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913_3_pae_pgi | = 1207805 | 81 (0.840) | 18 (0.210) | 18/228 | 6.6 | 20.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | = 1209602 | 73 (0.860) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 4277187 = | 109 (1.130) | 20 (0.230) | 18/234 | 6.8 | 17.0% | coding (459/465 nt) noncoding (140/140 nt) |
soxR ryjA |
redox‑sensitive transcriptional activator of soxS; autorepressor novel sRNA, function unknown |
| ? | NC_000913_3_pae_pgi | 4277218 = | 98 (1.130) | noncoding (109/140 nt) | ryjA | novel sRNA, function unknown | |||||
| * | ? | NC_000913_3_pae_pgi | = 228744 | 46 (0.480) | 28 (0.300) | 19/248 | 6.9 | 39.0% | intergenic (+82/‑12) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | = 225895 | NA (NA) | 30 (0.330) | 19/246 | 6.9 | NA | noncoding (137/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | = 225899 | NA (NA) | noncoding (141/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_pgi | 3423823 = | NA (NA) | 27 (0.290) | 18/248 | 7.3 | 21.4% | intergenic (‑36/+57) | rrfD/rrlD | 5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_pae_pgi | = 3946688 | 104 (1.070) | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_pgi | 2726200 = | NA (NA) | 27 (0.290) | 18/248 | 7.3 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_pgi | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 87 (0.900) | 16 (0.190) | 14/228 | 7.9 | 17.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 73 (0.860) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||