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 46 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 699,722 | 0 | A | G | 51.5% | 13.0 / 101.4 | 66 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 47.3% | 99.6 / 235.7 | 146 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 45.3% | 78.5 / 212.0 | 137 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 4,479,790 | 0 | A | G | 36.1% | 146.9 / 29.0 | 83 | intergenic (+27/‑110) | PP_3958/PP_3959 | Na(+)/H(+) antiporter NhaA 2/Voltage‑gated chloride channel family protein |
| * | JE3692‑4 | 195,634 | 0 | C | T | 36.1% | 314.1 / 217.0 | 192 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 4,479,807 | 0 | G | C | 35.9% | 142.3 / 55.2 | 83 | intergenic (+44/‑93) | PP_3958/PP_3959 | Na(+)/H(+) antiporter NhaA 2/Voltage‑gated chloride channel family protein |
| * | JE3692‑4 | 5,999,970 | 0 | C | T | 32.5% | 154.8 / 73.6 | 80 | intergenic (+188/‑358) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,971 | 0 | A | G | 32.5% | 152.2 / 74.6 | 80 | intergenic (+189/‑357) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 32.4% | 59.5 / 13.9 | 37 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 196,351 | 0 | C | G | 32.1% | 308.2 / 222.9 | 187 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 5,999,987 | 0 | A | . | 32.0% | 194.9 / 104.5 | 75 | intergenic (+205/‑341) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,981 | 0 | T | C | 31.6% | 155.1 / 58.3 | 76 | intergenic (+199/‑347) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 1,904,632 | 0 | A | C | 31.2% | 152.4 / 20.7 | 77 | intergenic (+70/‑450) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase |
| * | JE3692‑4 | 5,999,965 | 0 | C | A | 30.6% | 165.2 / 70.2 | 72 | intergenic (+183/‑363) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 30.0% | 67.0 / 25.6 | 56 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 196,390 | 0 | T | C | 28.2% | 312.8 / 142.0 | 164 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 2,982,613 | 0 | C | A | 26.7% | 166.1 / 31.1 | 75 | intergenic (+101/+48) | PP_2603/PP_2604 | conserved protein of unknown function/major facilitator family transporter |
| * | JE3692‑4 | 4,479,797 | 0 | C | A | 26.5% | 194.6 / 20.9 | 83 | intergenic (+34/‑103) | PP_3958/PP_3959 | Na(+)/H(+) antiporter NhaA 2/Voltage‑gated chloride channel family protein |
| * | JE3692‑4 | 884,007 | 0 | C | T | 26.1% | 178.1 / 24.3 | 100 | intergenic (+245/‑83) | PP_0766/PP_0767 | conserved exported protein of unknown function/Transcriptional regulator, LuxR family |
| * | JE3692‑4 | 2,750,794 | 0 | A | G | 26.0% | 188.5 / 14.3 | 77 | intergenic (+5/+30) | PP_2399/PP_2400 | conserved protein of unknown function/conserved protein of unknown function |
| Marginal new junction evidence (lowest skew 10 of 301 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 5566684 | 0 (0.000) | 52 (0.460) +GCC |
40/186 | 3.1 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer |
| ? | JE3692‑4 | 5566685 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer | |||||
| * | ? | JE3692‑4 | = 4992729 | 1 (0.010) | 52 (0.460) +GGC |
39/186 | 3.2 | 98.2% | intergenic (‑24/+44) | PP_4387/PP_4388 | conserved exported protein of unknown function/Flagellar hook protein FlgE |
| ? | JE3692‑4 | 4992730 = | 1 (0.010) | intergenic (‑25/+43) | PP_4387/PP_4388 | conserved exported protein of unknown function/Flagellar hook protein FlgE | |||||
| * | ? | JE3692‑4 | = 1644999 | 0 (0.000) | 41 (0.350) | 34/190 | 4.2 | 100% | intergenic (‑258/‑188) | PP_1443/araE (Ppu opt) | DNA‑binding, ATP‑dependent protease/– |
| ? | JE3692‑4 | = 1652985 | 0 (0.000) | intergenic (+174/+34) | nahF (Ppu opt)/PP_1445 | –/carbohydrate‑selective porin | |||||
| * | ? | JE3692‑4 | = 611136 | NA (NA) | 12 (0.110) | 12/186 | 10.5 | NA | noncoding (237/1314 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 611169 | NA (NA) | noncoding (270/1314 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | 171653 = | NA (NA) | 9 (0.080) | 9/188 | 12.0 | NA | noncoding (265/1522 nt) | PP_16SA | 16S ribosomal RNA |
| ? | JE3692‑4 | 171682 = | NA (NA) | noncoding (294/1522 nt) | PP_16SA | 16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 2092023 = | NA (NA) | 9 (0.080) | 9/190 | 12.1 | NA | noncoding (628/1445 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | 2092043 = | NA (NA) | noncoding (648/1445 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | = 178786 | NA (NA) | 10 (0.090) | 8/182 | 12.3 | 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 | = 3012136 | 107 (0.920) | 8 (0.070) | 8/188 | 12.6 | 6.6% | coding (3085/3621 nt) | PP_2627 | conserved membrane protein of unknown function |
| ? | JE3692‑4 | = 3012162 | 121 (1.060) | coding (3111/3621 nt) | PP_2627 | conserved membrane protein of unknown function | |||||
| * | ? | JE3692‑4 | = 2556265 | NA (NA) | 8 (0.070) | 7/180 | 12.8 | NA | intergenic (+160/‑84) | PP_t36/PP_23SF | tRNA‑Ala/23S ribosomal RNA |
| ? | JE3692‑4 | = 2556295 | NA (NA) | intergenic (+190/‑54) | PP_t36/PP_23SF | tRNA‑Ala/23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 175674 | NA (NA) | 8 (0.070) | 7/184 | 13.0 | NA | noncoding (2472/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | = 175695 | NA (NA) | noncoding (2493/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||