mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 33 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 63.5% | 13.3 / 132.9 | 117 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 52.5% | 9.6 / 127.4 | 80 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 48.6% | 13.1 / 25.7 | 35 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 699,722 | 0 | A | G | 41.5% | 53.4 / 81.2 | 65 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 5,999,981 | 0 | T | C | 38.6% | 64.6 / 76.5 | 70 | intergenic (+199/‑347) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,987 | 0 | A | . | 38.0% | 175.5 / 118.1 | 71 | intergenic (+205/‑341) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 324,670 | 0 | C | T | 36.7% | 65.1 / 39.7 | 60 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| * | JE3692‑4 | 5,999,970 | 0 | C | T | 33.3% | 76.4 / 64.8 | 63 | intergenic (+188/‑358) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,971 | 0 | A | G | 33.3% | 86.4 / 61.2 | 63 | intergenic (+189/‑357) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,965 | 0 | C | A | 32.8% | 93.9 / 60.6 | 61 | intergenic (+183/‑363) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 195,634 | 0 | C | T | 32.7% | 202.4 / 116.0 | 113 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 5,301,739 | 0 | G | C | 31.2% | 55.3 / 15.3 | 34 | A244G (GCC→GGC) | PP_4663 | conserved transmembrane protein of unknown function |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 30.8% | 27.4 / 10.8 | 29 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 196,351 | 0 | C | G | 28.8% | 232.7 / 133.3 | 139 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 1,541,581 | 0 | C | T | 27.8% | 83.0 / 22.6 | 56 | intergenic (‑57/‑44) | PP_1351/PP_1352 | putative 2‑dehydropantoate 2‑reductase/UPF0234 protein PP_1352 |
| * | JE3692‑4 | 196,390 | 0 | T | C | 27.7% | 207.2 / 88.9 | 112 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 2,184,203 | 0 | T | C | 25.4% | 126.7 / 20.9 | 59 | N269N (AAT→AAC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 5,653,816 | 0 | C | G | 23.4% | 110.4 / 15.7 | 51 | A304G (GCC→GGC) | PP_4952 | ATP‑dependent RNA helicase, specific for 23S rRNA |
| * | JE3692‑4 | 353,600 | 0 | C | T | 23.3% | 131.9 / 20.9 | 75 | G244S (GGT→AGT) | PP_0294 | choline / betaine / carnitine ABC transporter ‑ ATP binding subunit |
| * | JE3692‑4 | 884,005 | 0 | C | T | 22.7% | 82.5 / 12.5 | 44 | intergenic (+243/‑85) | PP_0766/PP_0767 | conserved exported protein of unknown function/Transcriptional regulator, LuxR family |
| Marginal new junction evidence (lowest skew 10 of 824 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | 5556623 = | NA (NA) | 15 (0.250) | 13/184 | 4.0 | 88.8% | intergenic (‑687/+190) | PP_4877/PP_4879 | 30S ribosomal protein S6/23S rRNA (guanosine‑2'‑O‑)‑methyltransferase RlmB |
| ? | JE3692‑4 | 5556649 = | 2 (0.030) | intergenic (‑713/+164) | PP_4877/PP_4879 | 30S ribosomal protein S6/23S rRNA (guanosine‑2'‑O‑)‑methyltransferase RlmB | |||||
| * | ? | JE3692‑4 | = 2931154 | 0 (0.000) | 14 (0.230) | 13/184 | 4.0 | 100% | intergenic (‑270/+295) | PP_2563/PP_2564 | putative Antibiotic biosynthesis protein/putative Quercetin 2,3‑dioxygenase |
| ? | JE3692‑4 | = 2931180 | NA (NA) | intergenic (‑296/+269) | PP_2563/PP_2564 | putative Antibiotic biosynthesis protein/putative Quercetin 2,3‑dioxygenase | |||||
| * | ? | JE3692‑4 | = 2556265 | NA (NA) | 20 (0.340) | 13/182 | 4.0 | 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 | = 1298275 | NA (NA) | 14 (0.230) | 13/184 | 4.0 | NA | noncoding (1791/2040 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 1298301 | NA (NA) | noncoding (1817/2040 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | = 178786 | NA (NA) | 16 (0.270) | 13/184 | 4.0 | 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 | = 173119 | NA (NA) | 20 (0.340) | 13/182 | 4.0 | NA | intergenic (+209/‑84) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA |
| ? | JE3692‑4 | = 173149 | NA (NA) | intergenic (+239/‑54) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 171310 = | NA (NA) | 14 (0.230) | 12/186 | 4.3 | NA | intergenic (+491/‑79) | PP_0159/PP_16SA | putative CoA‑transferase family III/16S ribosomal RNA |
| ? | JE3692‑4 | 171332 = | NA (NA) | intergenic (+513/‑57) | PP_0159/PP_16SA | putative CoA‑transferase family III/16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 172148 = | NA (NA) | 17 (0.270) | 12/192 | 4.5 | NA | noncoding (760/1522 nt) | PP_16SA | 16S ribosomal RNA |
| ? | JE3692‑4 | 172169 = | NA (NA) | noncoding (781/1522 nt) | PP_16SA | 16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 5999847 | 44 (0.690) | 10 (0.170) | 10/178 | 4.7 | 21.4% | intergenic (+65/‑481) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | JE3692‑4 | 6000039 = | 33 (0.570) | intergenic (+257/‑289) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | 4314694 = | NA (NA) | 12 (0.200) | 10/184 | 4.9 | 42.7% | intergenic (+1040/‑260) | PP_3774/PP_5627 | conserved protein of unknown function/protein of unknown function |
| ? | JE3692‑4 | 4314720 = | 17 (0.270) | intergenic (+1066/‑234) | PP_3774/PP_5627 | conserved protein of unknown function/protein of unknown function | |||||