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 85 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AE015451_phaM1 | 699,722 | 0 | A | G | 51.1% | 112.1 / inf | 931 | intergenic (+115/‑129) | PP_t06 tRNA (tRNA‑Ala)/PP_23SD rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 1,327,121 | 0 | C | T | 50.3% | 939.0 / inf | 1721 | intergenic (+97/‑196) | PP_16SE rRNA (16S ribosomal RNA)/PP_23SE rRNA (23S ribosomal RNA) | –/– |
| * | AE015451_phaM1 | 4,348,705 | 0 | A | G | 50.1% | 1.3 / inf | 1513 | 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 | 47.8% | 40.1 / 49.2 | 129 | 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 | 47.1% | ‑6.2 / 28.8 | 51 | L428F (TTG→TTT) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 4,675,360 | 0 | T | G | 46.5% | 150.8 / 114.2 | 283 | intergenic (+59/+45) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 4,344,308 | 0 | G | A | 42.0% | 100.8 / 34.1 | 141 | intergenic (+39/‑117) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 195,634 | 0 | C | T | 36.1% | 1657.1 / inf | 1282 | T380T (ACC→ACT) | PP_0168 CDS (putative surface adhesion protein) | |
| * | AE015451_phaM1 | 5,222,994 | 0 | G | T | 35.6% | ‑3.2 / 10.7 | 45 | L435M (CTG→ATG) | PP_4603 CDS (transposase) | |
| * | AE015451_phaM1 | 5,737,756 | 0 | A | G | 33.2% | 316.5 / 104.6 | 277 | intergenic (+45/+26) | hutF CDS (probable formiminoglutamate deiminase)/PP_5037 CDS (lipocalin family lipoprotein) | –/– |
| * | AE015451_phaM1 | 5,097,240 | 0 | A | C | 32.1% | 268.3 / 16.0 | 196 | intergenic (+231/+61) | PP_mr66 ncRNA (P6)/acsA‑I CDS (acetyl‑CoA synthetase) | –/– |
| * | AE015451_phaM1 | 5,671,653 | 0 | C | T | 30.9% | 406.9 / 34.5 | 278 | intergenic (+72/‑98) | PP_4978 CDS (conserved protein of unknown function)/PP_4979 CDS (putative Periplasmic binding protein) | –/– |
| * | AE015451_phaM1 | 4,889,623 | 0 | A | G | 30.8% | 250.7 / 29.0 | 162 | intergenic (+69/‑84) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 2,178,568 | 0 | G | A | 30.7% | 2466.9 / inf | 1334 | T268T (ACG→ACA) | PP_1931 CDS (conserved protein of unknown function) | |
| * | AE015451_phaM1 | 4,889,644 | 0 | G | C | 30.2% | 571.4 / 137.3 | 274 | intergenic (+90/‑63) | hyi CDS (hydroxypyruvate isomerase)/glxR CDS (tartronate semialdehyde reductase) | –/– |
| * | AE015451_phaM1 | 4,675,336 | 0 | T | G | 29.9% | 317.0 / 22.2 | 243 | intergenic (+35/+69) | PP_4137 CDS (putative Outer membrane siderophore receptor)/chrR CDS (Chromate reductase) | –/– |
| * | AE015451_phaM1 | 1,210,849 | 0 | A | C | 29.3% | 1148.2 / 89.9 | 585 | *540G (TGA→GGA) | PP_1060 CDS (putative Glutamate synthase_ large subunit) | |
| * | AE015451_phaM1 | 5,199,656 | 0 | G | T | 28.7% | 121.6 / 30.9 | 130 | intergenic (+31/+42) | PP_4579 CDS (Transcriptional regulator_ LysR family)/PP_4580 CDS (conserved protein of unknown function) | –/– |
| * | AE015451_phaM1 | 4,344,323 | 0 | G | A | 27.5% | 353.1 / 19.6 | 194 | intergenic (+54/‑102) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| * | AE015451_phaM1 | 4,344,296 | 0 | A | C | 27.4% | 298.3 / 27.4 | 198 | intergenic (+27/‑129) | PP_3817 CDS (Polyamine ABC transporter_ ATP‑binding protein)/PP_3818 CDS (Periplamic phosphate‑binding protein) | –/– |
| Marginal new junction evidence (lowest skew 10 of 298 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | 4808174 = | 63 (0.070) | 321 (0.480) | 46/200 | 4.4 | 59.1% | intergenic (‑283/‑272) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | = 5986211 | 398 (0.590) | intergenic (+229/‑317) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5555608 | 41 (0.050) | 296 (0.330) +GCC |
58/264 | 5.2 | 88.1% | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| ? | AE015451_phaM1 | 5555609 = | 41 (0.050) | intergenic (‑85/+86) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2472115 | 283 (0.310) | 115 (0.130) | 49/256 | 6.4 | 22.1% | intergenic (+19/+130) | PP_2166 CDS (Anti‑anti‑sigma factor)/PP_2167 CDS (putative PhoD‑like phosphatase) | –/– |
| ? | AE015451_phaM1 | 2472313 = | 543 (0.630) | coding (1783/1851 nt) | PP_2167 CDS (putative PhoD‑like phosphatase) | ||||||
| * | ? | AE015451_phaM1 | = 5681415 | 3 (0.000) | 262 (0.300) +CGGG |
38/262 | 9.1 | 98.9% | 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 | = 5201567 | 356 (0.390) | 71 (0.080) | 33/264 | 10.6 | 21.3% | intergenic (‑53/‑127) | PP_4582 CDS (conserved membrane protein of unknown function)/PP_4583 CDS (putative Peptidase) | –/– |
| ? | AE015451_phaM1 | 5201666 = | 177 (0.200) | intergenic (‑152/‑28) | PP_4582 CDS (conserved membrane protein of unknown function)/PP_4583 CDS (putative Peptidase) | –/– | |||||
| * | ? | AE015451_phaM1 | = 652782 | 716 (0.790) | 97 (0.130) | 25/230 | 11.4 | 24.1% | 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) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5699642 | 910 (1.000) | 56 (0.010) | 25/248 | 12.3 | 11.8% | 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 | = 4808176 | 56 (0.060) | 42 (0.050) | 25/254 | 12.7 | 18.0% | intergenic (‑285/‑270) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– |
| ? | AE015451_phaM1 | 4808280 = | 329 (0.380) | intergenic (‑389/‑166) | PP_4234 CDS (Aldehyde oxidase and xanthine dehydrogenase)/dsbD‑II CDS (thiol_disulfide interchange protein 2) | –/– | |||||
| * | ? | AE015451_phaM1 | 2478409 = | 996 (1.100) | 32 (0.040) | 19/218 | 13.0 | 3.9% | coding (106/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | |
| ? | AE015451_phaM1 | = 2478405 | 776 (1.060) | coding (102/444 nt) | PP_2172 CDS (conserved exported protein of unknown function) | ||||||
| * | ? | AE015451_phaM1 | = 5986033 | 534 (0.590) | 45 (0.050) | 23/254 | 13.4 | 8.4% | intergenic (+51/‑495) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– |
| ? | AE015451_phaM1 | 5986255 = | 477 (0.560) | intergenic (+273/‑273) | kefB‑III CDS (glutathione‑regulated potassium_H+ antiporter)/PP_mr64 ncRNA (C4 ncRNA) | –/– | |||||