mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 64.7% | 10.0 / 45.8 | 51 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 50.0% | ‑4.1 / 50.8 | 36 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 46.8% | 27.1 / 85.9 | 63 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,353,192 | 0 | C | A | 43.8% | 21.3 / 10.4 | 35 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 195,634 | 0 | C | T | 41.5% | 93.5 / 159.9 | 143 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,559 | 0 | C | A | 35.6% | 106.5 / 91.1 | 89 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 32.4% | 135.8 / 105.0 | 105 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,327 | 0 | A | C | 28.0% | 172.2 / 98.3 | 118 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 441,326 | 0 | G | . | 27.9% | 170.8 / 68.4 | 68 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 196,390 | 0 | T | C | 27.9% | 111.1 / 55.9 | 79 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,306 | 0 | T | C | 26.5% | 185.6 / 81.1 | 119 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,348,868 | 0 | C | A | 25.0% | 65.4 / 11.2 | 33 | L359M (CTG→ATG) | PP_2065 | multidrug RND transporter |
| * | NC_002947 | 5,831,886 | 0 | A | C | 24.5% | 505.8 / 29.4 | 243 | P86P (CCT→CCG) | ftsY | signal recognition particle protein translocation receptor GTPase |
| * | NC_002947 | 5,015,892 | 1 | . | A | 23.8% | 41.1 / 19.3 | 21 | intergenic (‑155/+79) | PP_5679/PP_4421 | hypothetical protein/aminotransferase |
| * | NC_002947 | 2,348,874 | 0 | G | T | 23.5% | 70.5 / 12.2 | 34 | A361S (GCG→TCG) | PP_2065 | multidrug RND transporter |
| * | NC_002947 | 2,348,891 | 0 | G | A | 21.9% | 61.0 / 10.9 | 34 | P366P (CCG→CCA) | PP_2065 | multidrug RND transporter |
| * | NC_002947 | 5,988,905 | 0 | T | C | 21.2% | 61.4 / 12.9 | 34 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,831,881 | 0 | A | C | 21.0% | 566.9 / 28.8 | 254 | V88G (GTA→GGA) | ftsY | signal recognition particle protein translocation receptor GTPase |
| * | NC_002947 | 4,583,571 | 0 | G | . | 20.6% | 87.5 / 20.7 | 34 | intergenic (‑144/+27) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| * | NC_002947 | 5,988,911 | 0 | A | . | 20.6% | 85.5 / 22.1 | 34 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 48 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 401301 | NA (NA) | 6 (0.090) | 6/272 | 3.6 | 13.9% | coding (887/1059 nt) | PP_0334 | transposase |
| ? | NC_002947 | 401364 = | 39 (0.570) | coding (950/1059 nt) | PP_0334 | transposase | |||||
| * | ? | NC_002947 | 1467704 = | 141 (2.050) | 5 (0.080) | 5/262 | 3.8 | 3.7% | coding (988/1479 nt) | algE | alginate production protein AlgE |
| ? | NC_002947 | = 1467700 | 132 (2.090) | coding (992/1479 nt) | algE | alginate production protein AlgE | |||||
| * | ? | NC_002947 | = 1835105 | 33 (0.480) | 4 (0.060) | 4/268 | 4.1 | 9.4% | coding (454/495 nt) | PP_1639 | SprT family protein |
| ? | NC_002947 | = 1835165 | 46 (0.710) | coding (394/495 nt) | PP_1639 | SprT family protein | |||||
| * | ? | NC_002947 | 564368 = | 34 (0.490) | 4 (0.060) | 4/266 | 4.1 | 10.7% | intergenic (+20/‑153) | rplQ/katA | 50S ribosomal protein L17/catalase |
| ? | NC_002947 | 564393 = | 35 (0.550) | intergenic (+45/‑128) | rplQ/katA | 50S ribosomal protein L17/catalase | |||||
| * | ? | NC_002947 | = 4953692 | 80 (1.160) | 4 (0.060) | 4/276 | 4.2 | 5.3% | coding (740/1692 nt) | PP_4363 | two‑component system sensor histidine kinase/response regulator |
| ? | NC_002947 | = 4953758 | 66 (0.990) | coding (674/1692 nt) | PP_4363 | two‑component system sensor histidine kinase/response regulator | |||||
| * | ? | NC_002947 | = 3968879 | NA (NA) | 6 (0.090) | 4/272 | 4.2 | 13.6% | coding (1007/1179 nt) | PP_3498 | transposase |
| ? | NC_002947 | 3968942 = | 40 (0.580) | coding (1070/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947 | = 2297165 | 99 (1.440) | 4 (0.060) | 4/272 | 4.2 | 4.2% | coding (2957/3645 nt) | sbcC | exonuclease subunit SbcC |
| ? | NC_002947 | = 2297200 | 88 (1.340) | coding (2922/3645 nt) | sbcC | exonuclease subunit SbcC | |||||
| * | ? | NC_002947 | = 4587997 | 47 (0.680) | 3 (0.050) | 3/258 | 4.4 | 5.8% | intergenic (‑183/‑139) | PP_4063/ivd | long‑chain fatty acid‑‑CoA ligase/isovaleryl‑CoA dehydrogenase |
| ? | NC_002947 | = 4588058 | 55 (0.880) | intergenic (‑244/‑78) | PP_4063/ivd | long‑chain fatty acid‑‑CoA ligase/isovaleryl‑CoA dehydrogenase | |||||
| * | ? | NC_002947 | = 2054725 | 76 (1.100) | 4 (0.060) | 3/260 | 4.4 | 5.6% | intergenic (‑100/‑135) | PP_1829/aroC | alpha/beta family hydrolase/chorismate synthase |
| ? | NC_002947 | = 2054761 | 67 (1.070) | intergenic (‑136/‑99) | PP_1829/aroC | alpha/beta family hydrolase/chorismate synthase | |||||
| * | ? | NC_002947 | 726896 = | 31 (0.450) | 3 (0.050) | 3/258 | 4.4 | 7.1% | intergenic (‑143/+124) | PP_0620/PP_0621 | GntR family transcriptional regulator/hypothetical protein |
| ? | NC_002947 | 726983 = | 50 (0.800) | intergenic (‑230/+37) | PP_0620/PP_0621 | GntR family transcriptional regulator/hypothetical protein | |||||