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 83 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 | 57.1% | ‑5.1 / 13.1 | 28 | L435M (CTG→ATG) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 1,327,121 | 0 | C | T | 53.2% | 544.2 / inf | 1547 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 699,722 | 0 | A | G | 51.9% | 190.0 / inf | 847 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 48.4% | 194.0 / inf | 1352 | intergenic (‑70/+404) | PP_3820 CDS (Group II intron‑encoding maturase)/galU CDS (UTP‑glucose‑1‑phosphate uridylyltransferase) | –/– |
| * | AE015451_phaM1 | 4,344,312 | 0 | G | A | 45.8% | 44.8 / 23.0 | 93 | intergenic (+43/‑113) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 5,223,013 | 0 | C | A | 42.9% | ‑6.4 / 24.9 | 35 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 40.9% | 133.9 / 100.3 | 209 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 4,675,360 | 0 | T | G | 39.1% | 208.1 / 47.6 | 193 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 37.1% | 1245.4 / inf | 1006 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 5,485,153 | 0 | A | G | 32.1% | 70.0 / 12.5 | 55 | intergenic (+59/‑88) | purH CDS (phosphoribosylaminoimidazolecarboxamide formyltransferase_IMP cyclohydrolase)/purD CDS (Phosphoribosylamine‑‑glycine ligase) | –/– |
| * | AE015451_phaM1 | 5,097,240 | 0 | A | C | 30.9% | 207.8 / 12.9 | 145 | intergenic (+231/+61) | PP_mr66 ncRNA (P6)/acsA‑I CDS (acetyl‑CoA synthetase) | –/– |
| * | AE015451_phaM1 | 5,199,657 | 0 | C | T | 30.1% | 88.3 / 12.9 | 110 | intergenic (+32/+41) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 2,178,568 | 0 | G | A | 29.3% | 2028.9 / inf | 1082 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 29.1% | 221.7 / 23.5 | 141 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 2,241,305 | 0 | T | G | 28.8% | 406.0 / 46.8 | 285 | intergenic (+52/‑229) | gltX CDS (Glutamate‑‑tRNA ligase)/PP_t25 tRNA (tRNA‑Ala) | –/– |
| * | AE015451_phaM1 | 5,199,655 | 0 | C | T | 28.2% | 104.7 / 22.0 | 110 | intergenic (+30/+43) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 27.8% | 110.1 / 14.3 | 104 | intergenic (+39/‑117) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 4,467,646 | 0 | A | G | 27.7% | 1283.2 / 100.0 | 664 | intergenic (+27/‑110) | nhaA‑II CDS (Na(+)_H(+) antiporter NhaA 2)/PP_3959 CDS (Voltage‑gated chloride channel family protein) | –/– |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 27.6% | 486.5 / 93.3 | 238 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 5,199,656 | 0 | G | T | 26.7% | 90.9 / 27.8 | 110 | intergenic (+31/+42) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| Marginal new junction evidence (lowest skew 10 of 304 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | = 1780066 | 236 (0.310) | 166 (0.230) | 64/256 | 3.4 | 44.9% | 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 = | 183 (0.250) | 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 | 29 (0.040) | 233 (0.310) +GCC |
53/264 | 5.2 | 89.1% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 29 (0.040) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2472115 | 276 (0.360) | 102 (0.140) | 49/256 | 5.5 | 22.6% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 437 (0.610) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | AE015451_phaM1 | 4808174 = | 59 (0.080) | 195 (0.350) | 35/200 | 5.8 | 50.2% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 343 (0.610) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | pS4413_qbsFH | 1 = | 0 (0.000) | 10375 (0.870) | 183/270 | 5.9 | 100% | intergenic (–/‑1952) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | = 5211 | 0 (0.000) | intergenic (‑521/–) | rep CDS/– | –/– | |||||
| * | ? | AE015451_phaM1 | = 652782 | 547 (0.720) | 112 (0.170) | 34/230 | 7.5 | 32.4% | coding (1961/1962 nt) | ctpL CDS (Methyl‑accepting chemotaxis protein CtpL) | |
| ? | AE015451_phaM1 | = 4808159 | 1 (0.000) | intergenic (‑268/‑287) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– | |||||
| * | ? | pS4413_qbsFH | = 81 | 29 (0.000) | 8028 (0.700) +GCCGC |
157/248 | 7.8 | 99.7% | intergenic (–/‑1872) | –/aadA CDS | –/– |
| ? | pS4413_qbsFH | 82 = | 29 (0.000) | intergenic (–/‑1871) | –/aadA CDS | –/– | |||||
| * | ? | AE015451_phaM1 | = 4808179 | 26 (0.030) | 94 (0.150) | 26/230 | 9.6 | 30.6% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986225 | 404 (0.630) | intergenic (+243/‑303) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5681415 | 3 (0.000) | 183 (0.250) +CGGG |
31/262 | 9.7 | 98.4% | 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 | 26 (0.030) | 96 (0.140) | 28/246 | 9.8 | 30.3% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | 5986041 = | 417 (0.600) | intergenic (+59/‑487) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||