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 | 4,037,225 | 0 | A | . | 44.4% | 4.9 / 11.8 | 10 | intergenic (+8/‑35) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913_3_pae_pgi | 4,037,227 | 1 | . | T | 40.0% | 0.5 / 15.6 | 10 | intergenic (+10/‑33) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913_3_pae_pgi | 3,428,678 | 0 | A | T | 36.8% | 13.5 / 20.0 | 19 | noncoding (85/1542 nt) | rrsD | 16S ribosomal RNA of rrnD operon |
| * | NC_000913_3_pae_pgi | 3,428,679 | 0 | A | T | 36.8% | 13.5 / 20.0 | 19 | noncoding (84/1542 nt) | rrsD | 16S ribosomal RNA of rrnD operon |
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 29.3% | 377.1 / 192.9 | 246 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 28.4% | 320.2 / 156.7 | 169 | 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 | 28.3% | 248.4 / 154.3 | 173 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 27.4% | 286.6 / 111.9 | 164 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 3,959,515 | 0 | T | A | 20.5% | 286.8 / 72.3 | 117 | intergenic (+70/+17) | ilvC/ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| * | NC_000913_3_pae_pgi | 1,864,758 | 0 | G | A | 20.1% | 392.2 / 96.1 | 184 | intergenic (+24/+24) | yeaD/yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| * | NC_000913_3_pae_pgi | 3,941,892 | 0 | T | A | 20.0% | 46.8 / 10.1 | 25 | noncoding (85/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 999 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 2068406 | 537 (3.180) | 102 (0.700) | 67/216 | 1.9 | 17.0% | pseudogene (14/159 nt) | yoeH | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| ? | NC_000913_3_pae_pgi | = 2068411 | 535 (3.690) | pseudogene (9/159 nt) | yoeH | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 2068389 = | 422 (2.500) | 86 (0.590) | 54/216 | 3.5 | 16.4% | pseudogene (31/159 nt) | yoeH | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| ? | NC_000913_3_pae_pgi | 2068430 = | 516 (3.560) | intergenic (‑11/‑205) | yoeH/yoeA | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/CP4‑44 prophage; putative disrupted hemin or colicin receptor;Phage or Prophage Related; interrupted by IS2 and C‑terminal deletion | |||||
| * | ? | NC_000913_3_pae_pgi | 2090108 = | 803 (4.750) | 86 (0.570) | 51/224 | 4.3 | 10.8% | intergenic (+62/‑84) | hisL/hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| ? | NC_000913_3_pae_pgi | 2090141 = | 702 (4.670) | intergenic (+95/‑51) | hisL/hisG | his operon leader peptide/ATP phosphoribosyltransferase | |||||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 143 (0.850) | 32 (0.220) | 32/220 | 8.2 | 22.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 100 (0.680) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | = 2084199 | 837 (4.950) | 49 (0.310) | 31/234 | 9.2 | 6.0% | intergenic (+16/+27) | sbcB/yeeD | exodeoxyribonuclease I; exonuclease I/putative TusA family sulfurtransferase |
| ? | NC_000913_3_pae_pgi | = 2084205 | 759 (4.830) | intergenic (+22/+21) | sbcB/yeeD | exodeoxyribonuclease I; exonuclease I/putative TusA family sulfurtransferase | |||||
| * | ? | NC_000913_3_pae_pgi | 1552249 = | NA (NA) | 39 (0.250) | 29/228 | 9.5 | NA | noncoding (1/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 1552279 = | NA (NA) | noncoding (31/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_pgi | 1552071 = | NA (NA) | 38 (0.250) | 28/228 | 9.8 | NA | noncoding (1/97 nt) | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 1552279 = | NA (NA) | noncoding (31/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_pgi | = 2098422 | 625 (3.700) | 44 (0.280) | 29/236 | 9.9 | 7.0% | intergenic (‑121/+25) | wzzB/ugd | regulator of length of O‑antigen component of lipopolysaccharide chains/UDP‑glucose 6‑dehydrogenase |
| ? | NC_000913_3_pae_pgi | = 2098429 | 579 (3.660) | intergenic (‑128/+18) | wzzB/ugd | regulator of length of O‑antigen component of lipopolysaccharide chains/UDP‑glucose 6‑dehydrogenase | |||||
| * | ? | NC_000913_3_pae_pgi | 2097275 = | NA (NA) | 34 (0.210) | 30/242 | 9.9 | 5.4% | intergenic (+50/+46) | hisI/wzzB | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
| ? | NC_000913_3_pae_pgi | 2097299 = | 593 (3.650) | intergenic (+74/+22) | hisI/wzzB | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains | |||||
| * | ? | NC_000913_3_pae_pgi | 2075078 = | 585 (3.460) | 40 (0.250) | 28/236 | 10.2 | 6.6% | coding (300/1533 nt) | yeeR | CP4‑44 prophage; putative membrane protein |
| ? | NC_000913_3_pae_pgi | 2075101 = | 576 (3.640) | coding (323/1533 nt) | yeeR | CP4‑44 prophage; putative membrane protein | |||||