mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 130 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,549,483 | 0 | G | C | 66.7% | 8.3 / 10.6 | 15 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,332,076 | 0 | C | T | 59.5% | ‑6.2 / 43.4 | 42 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 445,108 | 0 | A | T | 57.9% | ‑6.4 / 19.5 | 19 | intergenic (+78/‑210) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 699,725 | 0 | A | G | 53.3% | ‑4.2 / 36.0 | 31 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 445,106 | 0 | C | A | 52.6% | ‑2.6 / 21.3 | 19 | intergenic (+76/‑212) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 1,018,201 | 0 | T | G | 52.6% | ‑3.7 / 17.3 | 19 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 445,110 | 0 | T | G | 50.0% | 3.4 / 28.9 | 20 | intergenic (+80/‑208) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 445,118 | 0 | G | A | 50.0% | 1.1 / 21.2 | 18 | intergenic (+88/‑200) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 50.0% | 14.0 / 80.4 | 58 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,490,159 | 0 | T | C | 50.0% | ‑5.3 / 11.0 | 12 | intergenic (+68/‑79) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 195,634 | 0 | C | T | 48.8% | 8.6 / 56.3 | 43 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,479,135 | 0 | T | C | 47.6% | ‑0.4 / 22.9 | 21 | intergenic (‑48/+132) | PP_2167/tal | PhoD‑like phosphatase/transaldolase |
| * | NC_002947 | 3,583,415 | 0 | T | A | 47.6% | 7.3 / 10.1 | 22 | intergenic (+100/‑224) | PP_3158/PP_5589 | hypothetical protein/rhs repeat‑associated core domain‑containing protein |
| * | NC_002947 | 445,125 | 0 | C | G | 47.1% | 0.8 / 21.6 | 17 | intergenic (+95/‑193) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 445,126 | 0 | T | C | 47.1% | 2.8 / 18.3 | 17 | intergenic (+96/‑192) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 445,127 | 0 | C | A | 47.1% | 0.2 / 19.3 | 17 | intergenic (+97/‑191) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 196,340 | 0 | A | . | 46.7% | 40.4 / 54.2 | 30 | coding (1846/26049 nt) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,479,140 | 0 | T | C | 45.0% | ‑0.5 / 20.9 | 21 | intergenic (‑53/+127) | PP_2167/tal | PhoD‑like phosphatase/transaldolase |
| * | NC_002947 | 2,479,154 | 0 | A | G | 45.0% | 2.0 / 19.5 | 20 | intergenic (‑67/+113) | PP_2167/tal | PhoD‑like phosphatase/transaldolase |
| * | NC_002947 | 445,123 | 0 | G | A | 44.4% | 7.7 / 16.8 | 18 | intergenic (+93/‑195) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| Marginal new junction evidence (lowest skew 10 of 121 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 5066932 = | 56 (2.070) | 7 (0.260) | 7/288 | 2.0 | 11.6% | coding (612/1098 nt) | PP_4459 | transposase |
| ? | NC_002947 | 5066964 = | 52 (1.960) | coding (644/1098 nt) | PP_4459 | transposase | |||||
| * | ? | NC_002947 | = 953223 | 26 (0.960) | 6 (0.230) | 6/288 | 2.3 | 19.8% | coding (29/624 nt) | cyoC | cytochrome bo terminal oxidase subunit III |
| ? | NC_002947 | = 953241 | 23 (0.870) | coding (47/624 nt) | cyoC | cytochrome bo terminal oxidase subunit III | |||||
| * | ? | NC_002947 | 4962552 = | 31 (1.150) | 6 (0.250) | 5/264 | 2.4 | 16.9% | intergenic (‑41/+122) | fliH/fliG | flagellar assembly protein FliH/flagellar motor switch protein |
| ? | NC_002947 | 4962642 = | 31 (1.280) | intergenic (‑131/+32) | fliH/fliG | flagellar assembly protein FliH/flagellar motor switch protein | |||||
| * | ? | NC_002947 | = 1859742 | 27 (1.000) | 7 (0.280) | 5/270 | 2.4 | 19.0% | intergenic (+73/‑238) | PP_1658/PP_1659 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1859773 | 35 (1.410) | intergenic (+104/‑207) | PP_1658/PP_1659 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 796843 | 33 (1.220) | 5 (0.210) | 4/262 | 2.7 | 14.4% | intergenic (+42/‑148) | PP_0681/PP_0682 | hypothetical protein/inner membrane protein |
| ? | NC_002947 | = 796881 | 30 (1.240) | intergenic (+80/‑110) | PP_0681/PP_0682 | hypothetical protein/inner membrane protein | |||||
| * | ? | NC_002947 | = 5215242 | 19 (0.700) | 4 (0.160) | 4/274 | 2.8 | 17.1% | intergenic (‑111/+67) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| ? | NC_002947 | = 5215279 | 21 (0.830) | intergenic (‑148/+30) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase | |||||
| * | ? | NC_002947 | 6039022 = | 20 (0.740) | 4 (0.150) | 4/284 | 2.9 | 16.2% | coding (340/1212 nt) | dfp | bifunctional 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase |
| ? | NC_002947 | 6039048 = | 22 (0.840) | coding (366/1212 nt) | dfp | bifunctional 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase | |||||
| * | ? | NC_002947 | 5441919 = | 22 (0.810) | 4 (0.160) | 4/280 | 2.9 | 17.4% | coding (637/837 nt) | PP_4775 | hypothetical protein |
| ? | NC_002947 | 5441973 = | 17 (0.660) | coding (583/837 nt) | PP_4775 | hypothetical protein | |||||
| * | ? | NC_002947 | 5115118 = | 33 (1.220) | 6 (0.230) | 4/282 | 2.9 | 17.0% | coding (585/1419 nt) | aroP‑II | aromatic amino acid transport protein |
| ? | NC_002947 | 5115157 = | 27 (1.040) | coding (546/1419 nt) | aroP‑II | aromatic amino acid transport protein | |||||
| * | ? | NC_002947 | 4733512 = | 21 (0.780) | 5 (0.190) | 4/284 | 2.9 | 19.5% | coding (153/885 nt) | sucD | succinyl‑CoA synthetase subunit alpha |
| ? | NC_002947 | 4733544 = | 21 (0.800) | coding (121/885 nt) | sucD | succinyl‑CoA synthetase subunit alpha | |||||