mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
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 | 4,185,642 | 0 | G | A | 61.8% | 121.0 / 125.5 | 140 | R98H (CGC→CAC) | rpoC | RNA polymerase, beta prime subunit |
| * | NC_000913 | 1,357,070 | 0 | A | C | 58.7% | 66.4 / 107.6 | 110 | L14R (CTT→CGT) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,370,188 | 0 | C | A | 53.9% | 46.8 / 177.1 | 154 | intergenic (+185/‑28) | pspE/ycjM | thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
| * | NC_000913 | 723,130 | 0 | C | A | 41.4% | 63.0 / 156.8 | 145 | V429L (GTG→TTG) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| * | NC_000913 | 1,490,668 | 0 | C | T | 37.3% | 97.4 / 106.7 | 123 | pseudogene (46/750 nt) | gapC | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| * | NC_000913 | 1,753,712 | 0 | A | T | 32.5% | 161.8 / 99.7 | 124 | I40N (ATT→AAT) | ydhV | putative oxidoreductase subunit |
| * | NC_000913 | 4,506,185 | 1 | . | A | 31.8% | 163.6 / 203.2 | 132 | coding (899/1119 nt) | yjhC | GFO/IDH/MOCA family putative oxidoreductase. NAD(P)‑dependent |
| * | NC_000913 | 4,296,191 | 0 | A | C | 31.1% | 38.0 / 29.6 | 64 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,296,190 | 0 | A | G | 31.0% | 46.9 / 28.5 | 64 | intergenic (+396/+246) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,186,542 | 0 | A | T | 30.1% | 192.9 / 101.2 | 137 | K398M (AAG→ATG) | rpoC | RNA polymerase, beta prime subunit |
| * | NC_000913 | 1,196,220 | 0 | C | T | 26.6% | 159.0 / 74.6 | 117 | H366H (CAC→CAT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,232 | 0 | C | T | 25.2% | 180.4 / 68.3 | 117 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,247 | 0 | A | G | 24.8% | 179.5 / 66.1 | 113 | L375L (TTA→TTG) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,245 | 0 | T | C | 24.1% | 185.7 / 66.5 | 114 | L375L (TTA→CTA) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,277 | 0 | C | T | 21.1% | 228.3 / 49.2 | 114 | N385N (AAC→AAT) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| * | NC_000913 | 1,196,280 | 0 | G | C | 20.3% | 269.1 / 65.1 | 114 | A386A (GCG→GCC) | icd | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 16 (0.120) | 51 (0.420) | 44/548 | 3.1 | 79.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 12 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2347239 | 71 (0.550) | 49 (0.440) | 39/502 | 3.2 | 44.7% | noncoding (80/203 nt) | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences |
| ? | NC_000913 | 2347328 = | 60 (0.540) | noncoding (169/203 nt) | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences | |||||
| * | ? | NC_000913 | 1207790 = | 24 (0.190) | 46 (0.380) | 41/548 | 3.6 | 71.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4542690 | 202 (1.560) | 18 (0.140) | 18/562 | 9.5 | 10.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 122 (0.970) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4542682 = | 200 (1.550) | 10 (0.080) | 9/562 | 13.7 | 6.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 122 (0.970) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 3658001 | 132 (1.020) | 6 (0.050) | 6/558 | 15.5 | 4.5% | intergenic (+434/‑365) | hdeD/gadE | acid‑resistance membrane protein/gad regulon transcriptional activator |
| ? | NC_000913 | = 3658004 | 128 (1.030) | intergenic (+437/‑362) | hdeD/gadE | acid‑resistance membrane protein/gad regulon transcriptional activator | |||||
| * | ? | NC_000913 | 3051047 = | 181 (1.400) | 6 (0.050) | 6/562 | 15.6 | 3.4% | intergenic (‑380/+68) | gcvT/ubiI | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent |
| ? | NC_000913 | 3051073 = | 167 (1.330) | intergenic (‑406/+42) | gcvT/ubiI | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent | |||||
| * | ? | NC_000913 | = 1460446 | 131 (1.010) | 5 (0.040) | 5/570 | 16.5 | 3.7% | coding (1393/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| ? | NC_000913 | = 1460450 | 129 (1.020) | coding (1397/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent | |||||
| * | ? | NC_000913 | 2304463 = | NA (NA) | 4 (0.040) +40 bp |
3/500 | 16.7 | 4.4% | noncoding (47/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2304987 | 102 (0.790) | noncoding (571/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 597090 = | 149 (1.150) | 4 (0.030) | 4/574 | 17.4 | 2.9% | intergenic (+117/‑41) | cusC/cusF | copper/silver efflux system, outer membrane component/periplasmic copper‑ and silver‑binding protein |
| ? | NC_000913 | 803339 = | 120 (0.940) | intergenic (+19/‑164) | ybhI/ybhJ | putative DASS family tricarboxylate or dicarboxylate transporter/aconitase family protein | |||||