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 32 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 | 72.0% | 104.5 / 44.4 | 51 | 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 | 72.0% | 105.8 / 45.8 | 51 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,464,191 | 0 | T | A | 56.2% | 1.0 / 10.1 | 17 | Q476L (CAG→CTG) | algX | alginate biosynthesis protein AlgX |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.0% | 2.4 / 149.2 | 98 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 48.2% | 91.9 / 236.0 | 170 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 48.1% | 42.4 / 171.2 | 129 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 47.4% | 0.6 / 11.5 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 47.1% | 51.2 / 172.2 | 122 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,462,375 | 0 | T | G | 46.4% | 18.7 / 10.5 | 38 | intergenic (+18/‑22) | PP_4795/holA | lipoprotein/DNA polymerase III subunit delta |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 41.7% | 11.8 / 10.4 | 27 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 41.5% | 55.5 / 18.8 | 54 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 661,661 | 0 | A | C | 35.7% | 57.8 / 23.0 | 42 | W432G (TGG→GGG) | PP_0569 | MATE efflux family protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 35.5% | 15.7 / 11.9 | 32 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 33.3% | 121.0 / 77.3 | 84 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 32.1% | 103.2 / 13.2 | 57 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 31.8% | 25.5 / 15.9 | 22 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 28.6% | 87.3 / 12.4 | 49 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 27.6% | 126.9 / 61.7 | 87 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 27.3% | 41.8 / 14.1 | 22 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 27.3% | 24.6 / 13.3 | 22 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Marginal new junction evidence (lowest skew 10 of 34 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 36 (0.470) | 20 (0.270) | 18/280 | 5.0 | 34.9% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 40 (0.540) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 3 (0.040) | 13 (0.220) | 8/220 | 6.9 | 43.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 32 (0.540) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 15 (0.200) +GCC |
12/284 | 7.0 | 93.9% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.080) | 11 (0.160) +CGGCGCTTCGCGG |
9/264 | 7.8 | 29.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 4946919 = | 52 (0.670) | intergenic (+576/+222) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 17 (0.220) | 10 (0.140) | 8/268 | 8.3 | 33.5% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 24 (0.340) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 7 (0.090) | 7 (0.100) | 7/266 | 8.8 | 20.2% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 49 (0.690) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5916999 | 24 (0.310) | 5 (0.080) | 5/234 | 9.0 | 20.3% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | = 5917039 | 20 (0.320) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 380855 | 21 (0.270) | 5 (0.080) | 5/244 | 9.3 | 25.2% | intergenic (+45/+64) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | = 380889 | 12 (0.180) | intergenic (+79/+30) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 39 (0.500) | 6 (0.080) | 6/272 | 9.5 | 10.8% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 62 (0.850) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 25 (0.320) | 3 (0.050) | 3/212 | 9.6 | 14.9% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 16 (0.280) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||