mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 55 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,749 | 0 | A | G | 50.0% | ‑4.6 / 24.9 | 22 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,921,591 | 0 | T | A | 45.8% | 1.3 / 32.1 | 24 | intergenic (+24/+37) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947 | 1,921,592 | 0 | T | A | 45.8% | 1.8 / 31.9 | 24 | intergenic (+25/+36) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947 | 699,725 | 0 | A | G | 45.7% | 7.6 / 39.4 | 35 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 37.5% | 38.9 / 36.5 | 40 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,072,818 | 0 | A | . | 36.8% | 34.6 / 22.9 | 19 | coding (689/1308 nt) | mdtA | multidrug transporter membrane fusion protein |
| * | NC_002947 | 4,072,822 | 1 | . | T | 35.0% | 18.2 / 28.6 | 20 | coding (685/1308 nt) | mdtA | multidrug transporter membrane fusion protein |
| * | NC_002947 | 5,655,692 | 0 | T | . | 34.4% | 64.8 / 36.3 | 33 | intergenic (‑96/+56) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 3,048,648 | 0 | A | C | 33.3% | 17.5 / 16.4 | 24 | intergenic (+60/‑236) | PP_2661/PP_2662 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 4,741,286 | 1 | . | T | 33.3% | 9.1 / 13.9 | 12 | intergenic (+477/+275) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 181,943 | 0 | C | T | 32.7% | 57.2 / 43.3 | 55 | noncoding (52/120 nt) | PP_5SB | 5S ribosomal RNA |
| * | NC_002947 | 322,135 | 0 | G | A | 32.6% | 53.5 / 37.6 | 49 | intergenic (+420/+38) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| * | NC_002947 | 322,142 | 0 | T | C | 32.6% | 49.2 / 35.3 | 46 | intergenic (+427/+31) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| * | NC_002947 | 5,655,682 | 0 | T | G | 32.4% | 36.5 / 30.3 | 37 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,655,687 | 0 | C | A | 32.4% | 44.7 / 24.9 | 34 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 3,520,124 | 0 | T | A | 31.2% | 15.1 / 10.6 | 16 | intergenic (+700/‑180) | PP_5580/PP_5582 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 5,903,220 | 0 | G | T | 31.0% | 29.3 / 19.0 | 29 | intergenic (‑128/‑140) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947 | 5,903,221 | 0 | A | C | 31.0% | 19.6 / 21.1 | 29 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 30.9% | 48.3 / 32.0 | 43 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,691,825 | 0 | C | A | 30.4% | 35.3 / 13.4 | 23 | intergenic (+50/‑121) | PP_1487/PP_1488 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Marginal new junction evidence (lowest skew 10 of 79 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 2295841 | 28 (1.060) | 6 (0.280) | 6/226 | 1.9 | 18.7% | intergenic (+44/+89) | PP_5496/PP_2023 | hypothetical protein/glutathione S‑transferase family protein |
| ? | NC_002947 | = 2295878 | 29 (1.330) | intergenic (+81/+52) | PP_5496/PP_2023 | hypothetical protein/glutathione S‑transferase family protein | |||||
| * | ? | NC_002947 | 1799893 = | 49 (1.850) | 6 (0.270) | 6/228 | 1.9 | 16.1% | intergenic (+21/‑166) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha |
| ? | NC_002947 | 1799981 = | 22 (1.000) | intergenic (+109/‑78) | rnhB/dnaEA | ribonuclease HII/DNA polymerase III subunit alpha | |||||
| * | ? | NC_002947 | 4091366 = | 30 (1.140) | 7 (0.270) | 7/264 | 2.0 | 19.7% | intergenic (+8/‑70) | gudP/garD | glucarate transporter/galactarate dehydratase |
| ? | NC_002947 | 4091395 = | 28 (1.100) | intergenic (+37/‑41) | gudP/garD | glucarate transporter/galactarate dehydratase | |||||
| * | ? | NC_002947 | 4159113 = | 29 (1.100) | 6 (0.250) | 6/248 | 2.1 | 19.3% | intergenic (+17/‑192) | PP_3661/PP_3662 | membrane protein/hypothetical protein |
| ? | NC_002947 | 4159201 = | 24 (1.000) | intergenic (+105/‑104) | PP_3661/PP_3662 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | 5210267 = | 35 (1.320) | 6 (0.260) | 5/242 | 2.3 | 18.5% | intergenic (‑85/+93) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| ? | NC_002947 | 5210358 = | 22 (0.940) | intergenic (‑176/+2) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase | |||||
| * | ? | NC_002947 | = 3999735 | 22 (0.830) | 6 (0.230) | 6/266 | 2.3 | 19.9% | coding (376/987 nt) | PP_3528 | ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 3999760 | 27 (1.050) | coding (401/987 nt) | PP_3528 | ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 4886181 = | 26 (0.980) | 4 (0.190) | 4/216 | 2.4 | 17.2% | intergenic (+15/+108) | PP_4295/PP_4296 | TetR family transcriptional regulator/hypothetical protein |
| ? | NC_002947 | 4886268 = | 18 (0.860) | intergenic (+102/+21) | PP_4295/PP_4296 | TetR family transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | = 1731232 | 24 (0.910) | 4 (0.190) | 4/218 | 2.4 | 17.0% | intergenic (‑103/+88) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | = 1731268 | 20 (0.950) | intergenic (‑139/+52) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 413997 = | 40 (1.510) | 5 (0.240) | 4/218 | 2.4 | 15.9% | intergenic (+14/‑189) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | 414083 = | 21 (1.000) | intergenic (+100/‑103) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | = 6019326 | 37 (1.400) | 5 (0.230) | 4/228 | 2.5 | 12.5% | intergenic (‑71/+74) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase |
| ? | NC_002947 | = 6019356 | 39 (1.770) | intergenic (‑101/+44) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase | |||||