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 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 60.0% | 32.5 / 24.8 | 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 59.1% | 35.2 / 29.2 | 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 5,558,407 | 0 | G | T | 55.6% | 12.3 / 24.0 | 18 | intergenic (‑68/+103) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 54.5% | 0.8 / 17.5 | 25 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,544,408 | 0 | T | G | 53.8% | 0.2 / 12.8 | 13 | G404G (GGT→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.3% | 18.3 / 162.9 | 118 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 48.8% | 67.0 / 183.7 | 129 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 48.6% | 3.4 / 27.5 | 38 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 48.1% | 3.5 / 11.1 | 27 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,440,082 | 0 | G | T | 47.8% | 15.0 / 14.9 | 23 | intergenic (‑413/‑246) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 47.1% | 2.9 / 21.8 | 35 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 46.9% | 19.0 / 13.6 | 33 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 42.4% | 16.7 / 10.0 | 34 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 40.0% | 99.3 / 123.3 | 121 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 117,271 | 0 | A | T | 36.8% | 20.1 / 11.4 | 45 | intergenic (+51/+43) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 35.7% | 15.1 / 11.3 | 14 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 35.7% | 34.8 / 10.1 | 44 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 34.8% | 50.1 / 10.1 | 47 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 34.8% | 66.2 / 13.5 | 48 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 1,703,248 | 0 | A | G | 34.5% | 24.6 / 24.0 | 29 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 5 (0.070) | 19 (0.280) +GCC |
16/284 | 5.4 | 79.5% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 5 (0.070) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 28 (0.400) | 13 (0.190) | 13/280 | 6.2 | 27.1% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 43 (0.640) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 4 (0.060) | 12 (0.230) | 6/220 | 7.6 | 42.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 30 (0.570) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.030) | 11 (0.160) +CGGG |
9/282 | 7.9 | 85.0% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.030) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 7 (0.110) | 6/266 | 9.0 | 17.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 62 (0.970) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5861679 | 24 (0.340) | 4 (0.070) | 4/230 | 9.2 | 14.0% | intergenic (+42/+96) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein |
| ? | NC_002947_CJ‑RC | = 5861724 | 30 (0.540) | intergenic (+87/+51) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 6 (0.090) | 6 (0.090) | 6/276 | 9.3 | 52.8% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 5 (0.080) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 401301 | NA (NA) | 5 (0.080) | 5/276 | 9.9 | 10.4% | coding (887/1059 nt) | PP_0334 | transposase |
| ? | NC_002947_CJ‑RC | 401364 = | 45 (0.640) | coding (950/1059 nt) | PP_0334 | transposase | |||||
| * | ? | NC_002947_CJ‑RC | = 4895282 | 13 (0.190) | 4 (0.070) | 3/236 | 10.1 | 30.1% | intergenic (+54/‑154) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947_CJ‑RC | = 4895307 | 8 (0.140) | intergenic (+79/‑129) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947_CJ‑RC | 1114870 = | 33 (0.470) | 3 (0.050) | 3/240 | 10.2 | 11.5% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947_CJ‑RC | 1114946 = | 19 (0.330) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||