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 (highest frequency 20 of 77 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AE015451_phaM1 | 1,327,121 | 0 | C | T | 51.5% | 763.3 / inf | 1639 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 50.4% | 3.6 / inf | 1492 | intergenic (‑70/+404) | PP_3820 CDS (Group II intron‑encoding maturase)/galU CDS (UTP‑glucose‑1‑phosphate uridylyltransferase) | –/– |
| * | AE015451_phaM1 | 699,722 | 0 | A | G | 49.6% | 18.6 / inf | 959 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,675,360 | 0 | T | G | 47.1% | 210.7 / 76.5 | 246 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 4,344,312 | 0 | G | A | 36.9% | 45.0 / 38.9 | 109 | intergenic (+43/‑113) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 36.8% | 281.6 / 101.1 | 253 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 36.5% | 1623.4 / inf | 1241 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 36.1% | 189.3 / 25.8 | 135 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 35.8% | 101.0 / 31.6 | 123 | intergenic (+39/‑117) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 34.2% | 405.6 / 124.3 | 228 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 5,223,013 | 0 | C | A | 34.1% | ‑1.4 / 19.0 | 44 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 2,178,568 | 0 | G | A | 33.1% | 1961.8 / inf | 1167 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 1,210,830 | 0 | G | T | 29.8% | 1235.5 / 277.0 | 611 | intergenic (+20/+17) | ytnA CDS (Uncharacterized amino acid permease YtnA)/PP_1060 CDS (putative Glutamate synthase_ large subunit) | –/– |
| * | AE015451_phaM1 | 1,210,823 | 0 | C | G | 29.6% | 1272.3 / 244.0 | 601 | intergenic (+13/+24) | ytnA CDS (Uncharacterized amino acid permease YtnA)/PP_1060 CDS (putative Glutamate synthase_ large subunit) | –/– |
| * | AE015451_phaM1 | 614,285 | 0 | A | C | 29.6% | 374.6 / 44.9 | 245 | intergenic (‑104/+74) | dxs CDS (1‑deoxyxylulose‑5‑phosphate synthase)/ispA CDS (farnesyl diphosphate synthase) | –/– |
| * | AE015451_phaM1 | 1,210,849 | 0 | A | C | 29.3% | 1001.5 / 108.5 | 556 | *540G (TGA→GGA) | PP_1060 CDS (putative Glutamate synthase_ large subunit) | |
| * | AE015451_phaM1 | 4,675,336 | 0 | T | G | 29.1% | 229.3 / 17.5 | 186 | intergenic (+35/+69) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 2,241,305 | 0 | T | G | 28.9% | 414.3 / 55.3 | 308 | intergenic (+52/‑229) | gltX CDS (Glutamate‑‑tRNA ligase)/PP_t25 tRNA (tRNA‑Ala) | –/– |
| * | AE015451_phaM1 | 4,344,323 | 0 | G | A | 28.7% | 256.9 / 18.7 | 145 | intergenic (+54/‑102) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 4,353,193 | 0 | A | C | 28.4% | 263.6 / 34.9 | 226 | T107P (ACG→CCG) | yrpB CDS (2‑nitropropane dioxygenase) | |
| Marginal new junction evidence (lowest skew 10 of 232 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | = 1780066 | 233 (0.270) | 176 (0.220) | 69/256 | 3.9 | 43.6% | intergenic (+25/+81) | PP_1587 CDS (NhaP‑type Na+_H+ and K+_H+ antiporters)/dapC CDS (N‑succinyl‑L_L‑diaminopimelate aminotransferase alternative) | –/– |
| ? | AE015451_phaM1 | 1780129 = | 234 (0.290) | intergenic (+88/+18) | PP_1587 CDS (NhaP‑type Na+_H+ and K+_H+ antiporters)/dapC CDS (N‑succinyl‑L_L‑diaminopimelate aminotransferase alternative) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5699642 | 859 (1.010) | 3109 (0.990) | 65/248 | 4.1 | 88.7% | intergenic (+388/‑3617) | PP_5002 CDS (conserved protein of unknown function)/PP_5009 CDS (conserved protein of unknown function) | –/– |
| ? | pS4413_qbsFH | 12 = | 0 (0.000) | intergenic (–/‑1941) | –/aadA CDS | –/– | |||||
| * | ? | AE015451_phaM1 | = 5555608 | 47 (0.060) | 272 (0.330) +GCC |
56/264 | 6.2 | 85.5% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 47 (0.060) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5681415 | 1 (0.000) | 245 (0.300) +CGGG |
46/262 | 8.2 | 99.6% | intergenic (‑133/+71) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– |
| ? | AE015451_phaM1 | 5681416 = | 1 (0.000) | intergenic (‑134/+70) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– | |||||
| * | ? | AE015451_phaM1 | 4808174 = | 56 (0.070) | 225 (0.360) | 31/200 | 8.6 | 50.7% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 396 (0.630) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2472115 | 283 (0.330) | 113 (0.140) | 40/256 | 9.3 | 23.3% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 475 (0.590) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | AE015451_phaM1 | = 652782 | 609 (0.710) | 124 (0.170) | 30/230 | 10.8 | 32.3% | coding (1961/1962 nt) | ctpL CDS (Methyl‑accepting chemotaxis protein CtpL) | |
| ? | AE015451_phaM1 | = 4808159 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– | |||||
| * | ? | AE015451_phaM1 | 2478409 = | 891 (1.040) | 52 (0.080) | 26/218 | 11.4 | 6.8% | coding (106/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | |
| ? | AE015451_phaM1 | = 2478405 | 705 (1.020) | coding (102/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | ||||||
| * | ? | AE015451_phaM1 | = 4808179 | 25 (0.030) | 108 (0.150) | 25/230 | 12.5 | 31.0% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986225 | 460 (0.630) | intergenic (+243/‑303) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 4808179 | 25 (0.030) | 110 (0.140) | 27/246 | 12.7 | 30.6% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | 5986041 = | 475 (0.610) | intergenic (+59/‑487) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||