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 87 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AE015451_phaM1 | 5,222,994 | 0 | G | T | 54.5% | ‑4.8 / 15.5 | 33 | L435M (CTG→ATG) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 1,327,121 | 0 | C | T | 51.0% | 740.3 / inf | 1530 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,344,312 | 0 | G | A | 49.4% | 20.9 / 40.3 | 99 | intergenic (+43/‑113) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 699,722 | 0 | A | G | 49.3% | ‑4.7 / inf | 835 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 45.7% | 498.8 / inf | 1421 | 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 | 44.2% | 157.4 / 68.4 | 204 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 5,223,013 | 0 | C | A | 42.1% | ‑5.3 / 20.1 | 38 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 39.7% | 130.4 / 50.3 | 143 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 38.6% | 1307.9 / inf | 1215 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 38.5% | 326.6 / 131.8 | 229 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 38.2% | 209.3 / 86.5 | 213 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 37.1% | 77.5 / 25.3 | 110 | 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 | 32.3% | 2128.5 / inf | 1222 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 4,889,624 | 0 | G | T | 32.1% | 210.5 / 15.9 | 143 | intergenic (+70/‑83) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,889,619 | 0 | A | C | 29.4% | 172.3 / 30.5 | 137 | intergenic (+65/‑88) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 5,199,655 | 0 | C | T | 29.2% | 84.6 / 28.0 | 110 | intergenic (+30/+43) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 4,353,193 | 0 | A | C | 29.0% | 336.0 / 42.3 | 276 | T107P (ACG→CCG) | yrpB CDS (2‑nitropropane dioxygenase) | |
| * | AE015451_phaM1 | 5,344,486 | 0 | T | G | 28.5% | 291.5 / 45.9 | 211 | intergenic (+61/‑117) | pgi‑II CDS (glucose‑6‑phosphate isomerase)/acsA‑II CDS (acetyl‑CoA synthetase) | –/– |
| * | AE015451_phaM1 | 195,559 | 0 | C | A | 27.5% | 2228.6 / inf | 963 | T355T (ACC→ACA) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 5,344,454 | 0 | T | G | 27.4% | 420.8 / 35.3 | 244 | intergenic (+29/‑149) | pgi‑II CDS (glucose‑6‑phosphate isomerase)/acsA‑II CDS (acetyl‑CoA synthetase) | –/– |
| Marginal new junction evidence (lowest skew 10 of 215 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | = 5555608 | 43 (0.050) | 261 (0.340) +GCC |
62/264 | 3.7 | 86.1% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 43 (0.050) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | AE015451_phaM1 | 4808174 = | 59 (0.070) | 247 (0.420) | 36/200 | 5.4 | 57.7% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 319 (0.540) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2472115 | 287 (0.360) | 102 (0.140) | 48/256 | 5.4 | 21.6% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 470 (0.630) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | pS4413_qbsFH | 1 = | 0 (0.000) | 13318 (0.870) | 188/270 | 5.5 | 100% | intergenic (–/‑1952) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | = 5211 | 0 (0.000) | intergenic (‑521/–) | rep CDS/– | –/– | |||||
| * | ? | AE015451_phaM1 | = 652782 | 586 (0.740) | 129 (0.190) | 37/230 | 6.5 | 34.0% | coding (1961/1962 nt) | ctpL CDS (Methyl‑accepting chemotaxis protein CtpL) | |
| ? | AE015451_phaM1 | = 4808159 | 2 (0.000) | intergenic (‑268/‑287) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5681415 | 3 (0.000) | 192 (0.250) +CGGG |
38/262 | 7.5 | 98.5% | intergenic (‑133/+71) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– |
| ? | AE015451_phaM1 | 5681416 = | 3 (0.000) | intergenic (‑134/+70) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– | |||||
| * | ? | AE015451_phaM1 | = 4808179 | 18 (0.020) | 109 (0.160) | 30/230 | 8.1 | 34.6% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986225 | 397 (0.590) | intergenic (+243/‑303) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | pS4413_qbsFH | = 81 | 41 (0.000) | 10793 (0.730) +GCCGC |
156/248 | 8.2 | 99.6% | intergenic (–/‑1872) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | 82 = | 41 (0.000) | intergenic (–/‑1871) | –/aadA CDS | –/– | |||||
| * | ? | AE015451_phaM1 | = 4808179 | 18 (0.020) | 109 (0.150) | 30/246 | 8.8 | 33.8% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | 5986041 = | 410 (0.570) | intergenic (+59/‑487) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | 2478409 = | 861 (1.090) | 37 (0.060) | 25/218 | 8.9 | 5.2% | coding (106/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | |
| ? | AE015451_phaM1 | = 2478405 | 657 (1.030) | coding (102/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | ||||||