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 53 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 51.3% | 27.9 / 202.6 | 117 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 49.2% | 70.2 / 205.4 | 120 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 699,722 | 0 | A | G | 47.5% | 12.5 / 91.7 | 59 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 195,634 | 0 | C | T | 41.1% | 151.9 / 174.7 | 130 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 196,351 | 0 | C | G | 36.9% | 232.0 / 250.4 | 180 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 5,746,044 | 0 | G | C | 34.8% | 77.2 / 32.3 | 47 | G232G (GGC→GGG) | PP_5032 | Histidine ammonia‑lyase |
| * | JE3692‑4 | 196,390 | 0 | T | C | 34.0% | 240.2 / 161.6 | 156 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 2,184,200 | 0 | G | A | 33.9% | 101.3 / 23.5 | 61 | T268T (ACG→ACA) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 884,008 | 0 | A | G | 33.9% | 85.8 / 35.7 | 65 | intergenic (+246/‑82) | PP_0766/PP_0767 | conserved exported protein of unknown function/Transcriptional regulator, LuxR family |
| * | JE3692‑4 | 3,527,885 | 0 | T | C | 32.6% | 75.0 / 23.4 | 46 | D86D (GAT→GAC) | PP_5576 | conserved protein of unknown function |
| * | JE3692‑4 | 1,936,023 | 0 | C | G | 32.0% | 44.0 / 11.5 | 25 | intergenic (‑58/+47) | PP_1729/PP_1730 | conserved protein of unknown function/Probable M18 family aminopeptidase 2 |
| * | JE3692‑4 | 2,184,203 | 0 | T | C | 31.8% | 106.0 / 35.8 | 63 | N269N (AAT→AAC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 718,459 | 0 | A | C | 31.6% | 75.1 / 13.4 | 57 | intergenic (+29/+48) | PP_0612/PP_0613 | FAD‑dependent glycine/D‑amino acid oxidase/Amidase family protein |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 31.6% | 79.1 / 31.1 | 59 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 884,007 | 0 | C | T | 30.5% | 93.7 / 17.6 | 65 | intergenic (+245/‑83) | PP_0766/PP_0767 | conserved exported protein of unknown function/Transcriptional regulator, LuxR family |
| * | JE3692‑4 | 1,904,632 | 0 | A | C | 29.2% | 138.5 / 20.1 | 72 | intergenic (+70/‑450) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 28.9% | 62.2 / 10.7 | 38 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 5,735,358 | 0 | A | C | 28.2% | 86.1 / 12.2 | 39 | intergenic (‑184/+110) | PP_5024/PP_5025 | Amino acid ABC transporter, periplasmic amino acid‑binding protein/Glucans biosynthesis glucosyltransferase H |
| * | JE3692‑4 | 4,365,327 | 0 | C | G | 27.3% | 65.6 / 12.1 | 38 | G103G (GGC→GGG) | PP_3827 | 2‑nitropropane dioxygenase |
| * | JE3692‑4 | 196,327 | 0 | A | C | 26.9% | 333.3 / 156.8 | 176 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 181 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 5566684 | 1 (0.010) | 44 (0.520) +GCC |
29/192 | 3.1 | 97.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer |
| ? | JE3692‑4 | 5566685 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer | |||||
| * | ? | JE3692‑4 | 4820318 = | 0 (0.000) | 32 (0.500) | 20/146 | 3.3 | 54.2% | intergenic (‑283/‑272) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999855 = | 54 (0.850) | intergenic (+73/‑473) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 178786 | NA (NA) | 12 (0.150) | 10/188 | 8.5 | NA | noncoding (154/2902 nt) | PP_23SB | 23S ribosomal RNA |
| ? | JE3692‑4 | = 178803 | NA (NA) | noncoding (171/2902 nt) | PP_23SB | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 5213711 | 52 (0.600) | 12 (0.140) | 10/192 | 8.7 | 22.6% | intergenic (‑53/‑127) | PP_4582/PP_4583 | conserved membrane protein of unknown function/putative Peptidase |
| ? | JE3692‑4 | 5213810 = | 32 (0.380) | intergenic (‑152/‑28) | PP_4582/PP_4583 | conserved membrane protein of unknown function/putative Peptidase | |||||
| * | ? | JE3692‑4 | = 611136 | NA (NA) | 8 (0.100) | 7/192 | 10.2 | NA | noncoding (237/1314 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 611169 | NA (NA) | noncoding (270/1314 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | 175874 = | NA (NA) | 9 (0.110) | 7/190 | 10.2 | NA | noncoding (2672/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 175898 = | NA (NA) | noncoding (2696/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 5815749 | 101 (1.170) | 8 (0.090) | 7/196 | 10.4 | 7.5% | coding (536/882 nt) | PP_5083 | putative Type IV pili biogenesis protein PilM |
| ? | JE3692‑4 | = 5815776 | 97 (1.130) | coding (509/882 nt) | PP_5083 | putative Type IV pili biogenesis protein PilM | |||||
| * | ? | JE3692‑4 | = 171340 | 20 (0.230) | 7 (0.090) | 6/182 | 10.4 | 27.6% | intergenic (+521/‑49) | PP_0159/PP_16SA | putative CoA‑transferase family III/16S ribosomal RNA |
| ? | JE3692‑4 | = 176822 | NA (NA) | noncoding (4/1522 nt) | PP_16SB | 16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 171340 | 20 (0.230) | 7 (0.090) | 6/182 | 10.4 | 27.6% | intergenic (+521/‑49) | PP_0159/PP_16SA | putative CoA‑transferase family III/16S ribosomal RNA |
| ? | JE3692‑4 | = 171392 | NA (NA) | noncoding (4/1522 nt) | PP_16SA | 16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 4629981 | 66 (0.760) | 6 (0.070) | 6/190 | 10.7 | 8.8% | coding (4208/4593 nt) | PP_4085 | putative RHS family protein |
| ? | JE3692‑4 | = 4629992 | 61 (0.730) | coding (4219/4593 nt) | PP_4085 | putative RHS family protein | |||||