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 74 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AE015451_phaM1 | 5,223,013 | 0 | C | A | 53.5% | ‑5.6 / 46.5 | 43 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 699,722 | 0 | A | G | 52.2% | 202.2 / inf | 931 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 1,327,121 | 0 | C | T | 49.8% | 926.3 / inf | 1598 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 48.2% | 269.4 / inf | 1483 | intergenic (‑70/+404) | PP_3820 CDS (Group II intron‑encoding maturase)/galU CDS (UTP‑glucose‑1‑phosphate uridylyltransferase) | –/– |
| * | AE015451_phaM1 | 4,675,360 | 0 | T | G | 42.9% | 189.5 / 59.7 | 190 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 37.4% | 1436.2 / inf | 1176 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 34.4% | 261.2 / 89.7 | 224 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 196,879 | 0 | G | A | 33.9% | 197.1 / 145.1 | 168 | V795V (GTG→GTA) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 33.5% | 369.4 / 111.2 | 215 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 33.3% | 183.8 / 26.9 | 130 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 30.7% | 124.0 / 17.1 | 111 | intergenic (+39/‑117) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 2,178,568 | 0 | G | A | 30.3% | 2359.9 / inf | 1282 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 1,210,849 | 0 | A | C | 29.9% | 1055.6 / 106.6 | 556 | *540G (TGA→GGA) | PP_1060 CDS (putative Glutamate synthase_ large subunit) | |
| * | AE015451_phaM1 | 4,344,312 | 0 | G | A | 28.6% | 95.3 / 18.9 | 105 | intergenic (+43/‑113) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 1,210,830 | 0 | G | T | 27.9% | 1280.1 / 233.7 | 595 | intergenic (+20/+17) | ytnA CDS (Uncharacterized amino acid permease YtnA)/PP_1060 CDS (putative Glutamate synthase_ large subunit) | –/– |
| * | AE015451_phaM1 | 5,537,065 | 0 | T | G | 27.6% | 324.9 / 15.2 | 197 | intergenic (+42/+61) | nadE CDS (NH(3)‑dependent NAD(+) synthetase)/PP_4870 CDS (Azurin) | –/– |
| * | AE015451_phaM1 | 1,210,823 | 0 | C | G | 27.4% | 1332.6 / 209.4 | 581 | intergenic (+13/+24) | ytnA CDS (Uncharacterized amino acid permease YtnA)/PP_1060 CDS (putative Glutamate synthase_ large subunit) | –/– |
| * | AE015451_phaM1 | 4,675,334 | 0 | A | G | 27.2% | 241.6 / 12.6 | 150 | intergenic (+33/+71) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 5,671,671 | 0 | C | T | 27.1% | 519.8 / 33.4 | 315 | intergenic (+90/‑80) | PP_4978 CDS (conserved protein of unknown function)/PP_4979 CDS (putative Periplasmic binding protein) | –/– |
| * | AE015451_phaM1 | 5,199,657 | 0 | C | T | 26.6% | 82.0 / 29.9 | 127 | intergenic (+32/+41) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| Marginal new junction evidence (lowest skew 10 of 206 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | 4808174 = | 46 (0.060) | 317 (0.510) | 47/200 | 4.3 | 62.6% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 345 (0.560) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 1780066 | 283 (0.340) | 158 (0.200) | 62/256 | 4.4 | 42.7% | 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 = | 156 (0.200) | 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 | = 5555608 | 24 (0.030) | 250 (0.310) +GCC |
55/264 | 5.9 | 91.4% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 24 (0.030) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | pS4413_qbsFH | 1 = | 0 (0.000) | 16271 (0.910) | 189/270 | 7.1 | 100% | intergenic (–/‑1952) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | = 5211 | 0 (0.000) | intergenic (‑521/–) | rep CDS/– | –/– | |||||
| * | ? | pS4413_qbsFH | = 81 | 37 (0.000) | 12831 (0.740) +GCCGC |
158/248 | 10.2 | 99.7% | intergenic (–/‑1872) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | 82 = | 37 (0.000) | intergenic (–/‑1871) | –/aadA CDS | –/– | |||||
| * | ? | AE015451_phaM1 | = 5681415 | 2 (0.000) | 167 (0.210) +CGGG |
33/262 | 10.9 | 98.9% | intergenic (‑133/+71) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– |
| ? | AE015451_phaM1 | 5681416 = | 2 (0.000) | intergenic (‑134/+70) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– | |||||
| * | ? | AE015451_phaM1 | = 652782 | 624 (0.750) | 129 (0.180) | 27/230 | 11.1 | 32.7% | 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 = | 897 (1.070) | 47 (0.070) | 23/218 | 11.8 | 6.1% | coding (106/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | |
| ? | AE015451_phaM1 | = 2478405 | 729 (1.080) | coding (102/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | ||||||
| * | ? | AE015451_phaM1 | = 2472115 | 242 (0.290) | 48 (0.060) | 28/256 | 12.2 | 12.1% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 465 (0.590) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | AE015451_phaM1 | = 4808179 | 25 (0.030) | 113 (0.160) | 22/230 | 12.9 | 35.4% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986225 | 392 (0.550) | intergenic (+243/‑303) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||