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 30 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 | 69.0% | 53.0 / 28.3 | 31 | 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 | 69.0% | 47.5 / 28.8 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 62.5% | ‑0.2 / 16.0 | 34 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 55.2% | 14.2 / 126.2 | 105 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.4% | 12.7 / 173.1 | 126 | 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 | 51.7% | ‑6.7 / 17.1 | 32 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.5% | 50.3 / 197.9 | 136 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 46.2% | 31.0 / 50.6 | 108 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 41.0% | 21.2 / 11.6 | 41 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 117,271 | 0 | A | T | 36.2% | 53.3 / 16.5 | 55 | intergenic (+51/+43) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,531,676 | 0 | T | G | 35.7% | 57.9 / 12.1 | 42 | Q67P (CAG→CCG) | PP_1344 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,442,133 | 0 | T | G | 34.0% | 68.9 / 14.5 | 52 | Q13P (CAG→CCG) | rluE | 23S rRNA pseudouridine(2457) synthase |
| * | NC_002947_CJ‑RC | 1,403,591 | 0 | T | C | 33.3% | 8.7 / 12.2 | 20 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 30.8% | 95.8 / 26.5 | 113 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,798,322 | 0 | A | G | 29.2% | 28.3 / 11.4 | 27 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 251,249 | 0 | A | C | 27.9% | 76.5 / 19.2 | 44 | intergenic (‑47/‑19) | nfeD/PP_0201 | membrane bound peptidase NefD/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,903,730 | 0 | G | T | 27.0% | 80.6 / 10.8 | 37 | intergenic (+255/‑16) | PP_1703/nirB | assimilatory nitrate reductase/sulfite reductase/nitrite reductase large subunit |
| * | NC_002947_CJ‑RC | 4,798,317 | 0 | G | C | 26.9% | 38.9 / 19.1 | 27 | intergenic (‑172/+46) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 26.3% | 110.1 / 10.4 | 57 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 4,798,315 | 0 | C | T | 25.9% | 42.0 / 12.8 | 27 | intergenic (‑170/+48) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| Marginal new junction evidence (lowest skew 10 of 52 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.070) | 17 (0.280) | 12/220 | 5.7 | 38.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 49 (0.800) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 14 (0.180) +GCC |
14/284 | 6.9 | 93.5% | 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 | = 2957080 | 35 (0.430) | 13 (0.170) | 13/280 | 7.1 | 22.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 56 (0.720) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.060) | 14 (0.190) | 11/266 | 7.5 | 36.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 44 (0.590) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 52 (0.640) | 6 (0.100) | 6/220 | 8.5 | 14.2% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 33 (0.540) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | 5479905 = | 49 (0.610) | 5 (0.090) | 5/208 | 8.7 | 14.3% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947_CJ‑RC | 5480004 = | 25 (0.430) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.060) | 7 (0.100) | 6/250 | 9.5 | 18.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 58 (0.830) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1731167 | 24 (0.300) | 6 (0.080) | 6/276 | 10.2 | 16.5% | intergenic (‑80/+111) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947_CJ‑RC | 1731271 = | 38 (0.490) | intergenic (‑184/+7) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947_CJ‑RC | 5516057 = | 86 (1.060) | 4 (0.060) | 4/238 | 10.4 | 6.2% | intergenic (+20/‑134) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | 5516165 = | 50 (0.760) | intergenic (+128/‑26) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 6022085 | 39 (0.480) | 4 (0.060) | 4/244 | 10.6 | 12.2% | intergenic (‑71/+74) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase |
| ? | NC_002947_CJ‑RC | = 6022115 | 25 (0.370) | intergenic (‑101/+44) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase | |||||