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 84 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 | 51.8% | 785.6 / inf | 1705 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 49.5% | 99.0 / inf | 1449 | 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 | 47.9% | 75.6 / inf | 999 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 5,223,013 | 0 | C | A | 42.9% | ‑4.9 / 24.1 | 42 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 4,344,312 | 0 | G | A | 42.5% | 23.9 / 49.7 | 106 | intergenic (+43/‑113) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 40.7% | 157.8 / 39.5 | 141 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,675,360 | 0 | T | G | 36.5% | 221.2 / 57.5 | 206 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 36.3% | 1656.5 / inf | 1289 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 36.1% | 295.5 / 86.2 | 260 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 34.5% | 125.3 / 23.7 | 123 | 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 | 33.1% | 2226.2 / inf | 1296 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 32.6% | 481.1 / 134.0 | 266 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 5,199,656 | 0 | G | T | 32.3% | 87.0 / 40.8 | 133 | intergenic (+31/+42) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 445,112 | 0 | C | T | 31.8% | 167.1 / 11.9 | 89 | intergenic (+85/‑203) | PP_0367 CDS (conserved protein of unknown function)/PP_0368 CDS (putative Acyl‑CoA dehydrogenase) | –/– |
| * | AE015451_phaM1 | 5,485,153 | 0 | A | G | 31.7% | 136.5 / 14.7 | 88 | intergenic (+59/‑88) | purH CDS (phosphoribosylaminoimidazolecarboxamide formyltransferase_IMP cyclohydrolase)/purD CDS (Phosphoribosylamine‑‑glycine ligase) | –/– |
| * | AE015451_phaM1 | 5,199,657 | 0 | C | T | 29.9% | 94.8 / 28.1 | 132 | intergenic (+32/+41) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 4,344,323 | 0 | G | A | 29.1% | 242.3 / 17.5 | 147 | intergenic (+54/‑102) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 5,814,178 | 0 | C | T | 28.2% | 409.2 / 47.2 | 223 | intergenic (+88/+41) | PP_5092 CDS (putative exported NLP_P60 protein)/pilT CDS (twitching motility protein) | –/– |
| * | AE015451_phaM1 | 5,344,486 | 0 | T | G | 27.8% | 434.6 / 63.7 | 287 | intergenic (+61/‑117) | pgi‑II CDS (glucose‑6‑phosphate isomerase)/acsA‑II CDS (acetyl‑CoA synthetase) | –/– |
| * | AE015451_phaM1 | 1,210,839 | 0 | G | A | 27.3% | 1078.5 / 61.1 | 502 | intergenic (+29/+8) | ytnA CDS (Uncharacterized amino acid permease YtnA)/PP_1060 CDS (putative Glutamate synthase_ large subunit) | –/– |
| 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 | = 5555608 | 34 (0.040) | 301 (0.360) +GCC |
56/264 | 4.7 | 90.0% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 34 (0.040) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | AE015451_phaM1 | 4808174 = | 57 (0.070) | 251 (0.400) | 32/200 | 6.4 | 53.7% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 391 (0.620) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5681415 | 0 (0.000) | 237 (0.290) +CGGG |
43/262 | 6.7 | 100% | intergenic (‑133/+71) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– |
| ? | AE015451_phaM1 | 5681416 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986 CDS (Channel protein_ hemolysin III family)/PP_4987 CDS (putative Chemotaxis protein) | –/– | |||||
| * | ? | AE015451_phaM1 | = 652782 | 720 (0.840) | 136 (0.190) | 33/230 | 7.5 | 30.7% | 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 | = 2472115 | 215 (0.250) | 81 (0.100) | 36/256 | 7.9 | 20.5% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 424 (0.520) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | AE015451_phaM1 | = 4808179 | 10 (0.010) | 121 (0.160) | 29/246 | 9.2 | 30.8% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | 5986041 = | 536 (0.690) | intergenic (+59/‑487) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 4808179 | 10 (0.010) | 114 (0.160) | 25/230 | 9.6 | 32.6% | intergenic (‑288/‑267) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986225 | 463 (0.630) | intergenic (+243/‑303) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2282748 | 500 (0.580) | 48 (0.060) | 27/258 | 10.2 | 8.9% | intergenic (‑140/+89) | PP_2010 CDS (Cytochrome b561)/PP_2011 CDS (conserved exported protein of unknown function) | –/– |
| ? | AE015451_phaM1 | 2282815 = | 500 (0.610) | intergenic (‑207/+22) | PP_2010 CDS (Cytochrome b561)/PP_2011 CDS (conserved exported protein of unknown function) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5986033 | 573 (0.670) | 39 (0.050) | 26/254 | 10.4 | 7.0% | intergenic (+51/‑495) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– |
| ? | AE015451_phaM1 | 5986255 = | 491 (0.610) | intergenic (+273/‑273) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5201567 | 322 (0.380) | 31 (0.040) | 24/264 | 11.4 | 11.6% | intergenic (‑53/‑127) | PP_4582 CDS (conserved membrane protein of unknown function)/PP_4583 CDS (putative Peptidase) | –/– |
| ? | AE015451_phaM1 | 5201666 = | 157 (0.190) | intergenic (‑152/‑28) | PP_4582 CDS (conserved membrane protein of unknown function)/PP_4583 CDS (putative Peptidase) | –/– | |||||