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 27 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 | 699,722 | 0 | A | G | 53.6% | 7.2 / 146.4 | 112 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.9% | 41.2 / 200.1 | 140 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,952,675 | 0 | T | G | 42.9% | 11.1 / 27.9 | 28 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 42.7% | 72.7 / 131.2 | 103 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 40.0% | 39.6 / 26.5 | 20 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 39.5% | 97.3 / 124.0 | 119 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 35.0% | 26.0 / 13.4 | 20 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 32.5% | 28.8 / 10.5 | 41 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,952,676 | 0 | C | A | 32.0% | 42.7 / 10.6 | 28 | intergenic (‑123/+34) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 30.6% | 46.2 / 11.0 | 49 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 30.1% | 160.8 / 93.4 | 113 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 29.2% | 30.9 / 13.4 | 24 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,774 | 0 | G | C | 29.2% | 42.4 / 17.5 | 24 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 29.2% | 43.4 / 14.9 | 24 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 28.3% | 271.1 / 127.7 | 152 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,392,163 | 0 | G | T | 25.0% | 172.8 / 12.8 | 68 | intergenic (+549/‑173) | PP_4738/PP_mr56 | hypothetical protein/C4 ncRNA |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 24.5% | 317.7 / 138.8 | 164 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 24.5% | 278.9 / 99.8 | 160 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 197,590 | 0 | T | C | 24.2% | 284.2 / 95.3 | 149 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 24.1% | 55.4 / 17.4 | 29 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 27 (0.390) | 21/252 | 3.3 | 45.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 66 (0.960) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4647702 | 20 (0.270) | 4 (0.070) | 4/198 | 7.6 | 18.5% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | = 4647732 | 21 (0.390) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 27 (0.360) | 4 (0.070) | 4/198 | 7.6 | 16.6% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 21 (0.390) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 6022085 | 30 (0.400) | 5 (0.080) | 5/230 | 7.9 | 17.6% | intergenic (‑71/+74) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase |
| ? | NC_002947_CJ‑RC | = 6022115 | 22 (0.350) | intergenic (‑101/+44) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 6 (0.080) +GCC |
6/270 | 8.3 | 67.2% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 6080636 = | 50 (0.660) | 4 (0.060) | 4/228 | 8.4 | 12.4% | intergenic (‑123/+115) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter |
| ? | NC_002947_CJ‑RC | 6080736 = | 15 (0.240) | intergenic (‑223/+15) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 5762250 | 23 (0.310) | 3 (0.050) | 3/212 | 8.6 | 17.3% | intergenic (+44/+112) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | = 5762278 | 11 (0.190) | intergenic (+72/+84) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947_CJ‑RC | 5830630 = | 59 (0.780) | 4 (0.060) | 4/254 | 9.0 | 6.9% | intergenic (+17/+182) | mtgA/rpoH | monofunctional biosynthetic peptidoglycan transglycosylase/RNA polymerase factor sigma‑32 |
| ? | NC_002947_CJ‑RC | 5830738 = | 54 (0.780) | intergenic (+125/+74) | mtgA/rpoH | monofunctional biosynthetic peptidoglycan transglycosylase/RNA polymerase factor sigma‑32 | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 8 (0.110) | 6 (0.090) | 4/252 | 9.0 | 16.4% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 54 (0.790) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 4586141 = | 31 (0.410) | 3 (0.050) | 3/232 | 9.1 | 12.2% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | 4586212 = | 17 (0.270) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||