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 35 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 | 57.9% | 47.2 / 123.3 | 109 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.4% | 2.5 / 133.2 | 103 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 170,839 | 0 | T | G | 53.3% | 4.8 / 16.3 | 16 | intergenic (+20/‑550) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.7% | 57.0 / 215.1 | 147 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 316,025 | 0 | G | T | 50.0% | 6.5 / 11.1 | 22 | intergenic (+39/+44) | cysQ/PP_0262 | 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,668,053 | 0 | T | G | 41.7% | 2.3 / 14.0 | 12 | intergenic (+71/‑96) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 2,668,054 | 1 | . | T | 41.7% | 14.5 / 21.6 | 12 | intergenic (+72/‑95) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 41.0% | 22.3 / 11.5 | 39 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 36.3% | 77.9 / 27.8 | 97 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,668,062 | 0 | G | C | 35.7% | 20.5 / 12.7 | 14 | intergenic (+80/‑87) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 2,668,071 | 0 | G | C | 35.7% | 18.6 / 12.7 | 14 | intergenic (+89/‑78) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 441,318 | 0 | T | G | 34.2% | 43.2 / 16.1 | 41 | W67G (TGG→GGG) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 2,668,079 | 0 | A | . | 33.3% | 28.7 / 14.9 | 15 | intergenic (+97/‑70) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 2,668,081 | 0 | C | A | 33.3% | 24.9 / 11.4 | 15 | intergenic (+99/‑68) | prpF/prpD | aconitate isomerase/2‑methylcitrate dehydratase |
| * | NC_002947_CJ‑RC | 4,032,165 | 0 | C | A | 33.3% | 26.6 / 10.9 | 24 | intergenic (+58/‑198) | PP_3554/PP_3555 | acyl‑CoA dehydrogenase family protein/transmembrane sensor |
| * | NC_002947_CJ‑RC | 5,905,979 | 0 | G | T | 33.3% | 24.6 / 11.4 | 19 | intergenic (‑128/‑140) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 33.3% | 11.0 / 15.1 | 18 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 32.1% | 76.5 / 12.9 | 58 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 117,276 | 0 | C | G | 27.8% | 93.9 / 13.8 | 54 | intergenic (+56/+38) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 27.8% | 26.9 / 13.4 | 18 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 43 (0.600) | 13 (0.190) | 12/282 | 6.2 | 25.4% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 35 (0.500) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.120) | 5 (0.090) | 4/222 | 8.4 | 21.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 30 (0.550) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5479945 | 39 (0.540) | 7 (0.140) | 3/210 | 8.8 | 22.2% | intergenic (+43/+69) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 5479962 | 21 (0.410) | intergenic (+60/+52) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2050595 | 17 (0.240) | 3 (0.060) | 3/218 | 9.0 | 16.8% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2050631 | 17 (0.320) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 2233066 = | 28 (0.390) | 4 (0.070) | 4/246 | 9.1 | 13.9% | intergenic (+26/+205) | PP_1971/PP_t63 | hypothetical protein/tRNA‑Asn |
| ? | NC_002947_CJ‑RC | 2233158 = | 26 (0.430) | intergenic (+118/+113) | PP_1971/PP_t63 | hypothetical protein/tRNA‑Asn | |||||
| * | ? | NC_002947_CJ‑RC | 5290097 = | 63 (0.870) | 4 (0.070) | 3/232 | 9.4 | 7.9% | intergenic (‑75/+109) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290191 = | 43 (0.750) | intergenic (‑169/+15) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 380855 | 19 (0.260) | 3 (0.050) | 3/246 | 9.8 | 15.4% | intergenic (+45/+64) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | = 380889 | 17 (0.280) | intergenic (+79/+30) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5991572 | 37 (0.510) | 4 (0.060) | 4/276 | 9.9 | 8.5% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991794 = | 51 (0.750) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 3409265 = | 73 (1.010) | 4 (0.060) | 4/282 | 10.0 | 5.5% | coding (170/810 nt) | PP_3022 | AraC family transcriptional regulator |
| ? | NC_002947_CJ‑RC | 3409307 = | 68 (0.980) | coding (128/810 nt) | PP_3022 | AraC family transcriptional regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 358060 | 22 (0.300) | 4 (0.060) | 4/278 | 10.0 | 11.6% | intergenic (+28/‑102) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| ? | NC_002947_CJ‑RC | 358171 = | 40 (0.580) | coding (10/201 nt) | PP_5441 | hypothetical protein | |||||