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 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 | 697,094 | 0 | A | G | 55.6% | ‑1.1 / 12.8 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,466,841 | 0 | T | G | 52.2% | ‑6.3 / 14.8 | 23 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.7% | 34.6 / 206.5 | 146 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 50.0% | ‑2.5 / 12.4 | 29 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 47.9% | 17.0 / 205.1 | 143 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 47.4% | ‑6.4 / 12.3 | 19 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,952,675 | 0 | T | G | 43.5% | 8.0 / 11.1 | 25 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947_CJ‑RC | 1,842,816 | 0 | T | C | 42.9% | 5.6 / 12.2 | 23 | S660G (AGC→GGC) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 42.5% | 72.3 / 48.6 | 132 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 41.3% | 71.5 / 52.0 | 130 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 41.1% | 198.5 / 231.2 | 202 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 33.3% | 15.4 / 14.0 | 15 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 661,661 | 0 | A | C | 30.9% | 70.2 / 10.4 | 42 | W432G (TGG→GGG) | PP_0569 | MATE efflux family protein |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 29.5% | 132.6 / 28.3 | 137 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,049,907 | 0 | A | G | 27.3% | 26.7 / 12.2 | 24 | intergenic (+40/‑61) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 27.1% | 105.6 / 12.4 | 59 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 3,660,693 | 0 | T | G | 26.9% | 143.2 / 13.9 | 67 | V14V (GTA→GTC) | PP_3224 | class II aldolase/adducin domain‑containing protein |
| * | NC_002947_CJ‑RC | 3,207,678 | 0 | A | C | 26.8% | 169.1 / 16.7 | 82 | S443R (AGC→CGC) | PP_2812 | transporter |
| * | NC_002947_CJ‑RC | 2,051,065 | 0 | T | G | 26.2% | 107.2 / 10.4 | 65 | intergenic (‑63/+23) | PP_1825/PP_1826 | hypothetical protein/isochorismatase family hydrolase |
| * | NC_002947_CJ‑RC | 1,113,848 | 0 | T | G | 25.5% | 87.8 / 11.5 | 47 | intergenic (+43/+5) | hupN/rlmF | DNA‑binding protein HU/ribosomal RNA large subunit methyltransferase F |
| Marginal new junction evidence (lowest skew 10 of 31 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.070) | 32 (0.430) | 23/222 | 3.8 | 52.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 52 (0.700) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 67 (0.690) | 17 (0.200) | 14/252 | 7.5 | 37.0% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.040) | 19 (0.210) | 15/268 | 7.6 | 35.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 65 (0.730) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.020) | 16 (0.170) +GCC |
14/286 | 8.5 | 89.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.020) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 74 (0.760) | 8 (0.090) | 8/276 | 11.0 | 10.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 67 (0.730) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 39 (0.400) | 4 (0.060) | 4/214 | 11.3 | 11.2% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 35 (0.490) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 60 (0.610) | 6 (0.070) | 6/274 | 12.1 | 5.8% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 138 (1.510) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | 5384101 = | 78 (0.800) | 4 (0.050) | 3/222 | 12.4 | 7.6% | intergenic (+18/+115) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | 5384199 = | 38 (0.510) | intergenic (+116/+17) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | 5762219 = | 28 (0.290) | 3 (0.040) | 3/228 | 12.6 | 11.4% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | 5762311 = | 25 (0.330) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947_CJ‑RC | 5282598 = | 85 (0.870) | 3 (0.040) | 3/242 | 13.1 | 4.7% | intergenic (+28/+110) | trmA/pcaG | tRNA/tmRNA (uridine(54)‑C5)‑methyltransferase TrmA/protocatechuate 3,4‑dioxygenase subunit alpha |
| ? | NC_002947_CJ‑RC | 5282684 = | 52 (0.640) | intergenic (+114/+24) | trmA/pcaG | tRNA/tmRNA (uridine(54)‑C5)‑methyltransferase TrmA/protocatechuate 3,4‑dioxygenase subunit alpha | |||||