mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 28 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 | 5,558,423 | 2 | . | C | 88.9% | 23.4 / ‑2.7 | 9 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 88.9% | 22.5 / ‑2.7 | 9 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 100.0% | 11.0 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 100.0% | 11.0 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 73.3% | 50.9 / 24.9 | 30 | 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 | 1 | . | G | 70.4% | 45.1 / 24.3 | 30 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 55.0% | ‑3.9 / 14.0 | 21 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 53.9% | 9.9 / 131.7 | 102 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 337,809 | 0 | A | G | 53.3% | ‑5.5 / 14.1 | 15 | intergenic (‑59/+70) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,822 | 0 | C | G | 50.0% | 1.7 / 22.6 | 16 | intergenic (‑72/+57) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,825 | 0 | G | T | 50.0% | 3.6 / 19.4 | 15 | intergenic (‑75/+54) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,560,736 | 0 | T | G | 50.0% | 5.8 / 10.2 | 22 | intergenic (‑292/+39) | PP_4888/purA | methyl‑accepting chemotaxis transducer/adenylosuccinate synthetase |
| * | NC_002947_CJ‑RC | 337,816 | 1 | . | A | 46.7% | 11.6 / 33.5 | 15 | intergenic (‑66/+63) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,819 | 0 | A | C | 46.7% | 1.5 / 22.9 | 15 | intergenic (‑69/+60) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,827 | 0 | T | . | 43.8% | 24.7 / 23.9 | 16 | intergenic (‑77/+52) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 43.3% | 15.5 / 13.1 | 33 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 42.4% | 84.4 / 156.5 | 125 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 42.2% | 123.4 / 166.6 | 142 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 337,836 | 0 | C | T | 41.2% | 11.7 / 14.6 | 17 | intergenic (‑86/+43) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 37.1% | 26.0 / 10.6 | 40 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| 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 | = 2957080 | 43 (0.620) | 14 (0.210) | 13/280 | 6.0 | 27.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 33 (0.490) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.070) | 13 (0.200) | 10/266 | 6.7 | 44.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 28 (0.440) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 5 (0.070) | 13 (0.200) | 10/266 | 6.7 | 34.4% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 45 (0.710) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 5 (0.070) | 11 (0.170) | 8/266 | 7.6 | 32.6% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | 5789298 = | 41 (0.640) | intergenic (+26/‑105) | PP_5068/trxC | hypothetical protein/thioredoxin | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 5 (0.070) | 11 (0.170) | 8/266 | 7.6 | 34.6% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | 2301507 = | 37 (0.580) | intergenic (‑151/‑180) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1436099 | 52 (0.750) | 11 (0.170) | 8/266 | 7.6 | 29.4% | intergenic (‑136/+17) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947_CJ‑RC | 1499519 = | 5 (0.080) | intergenic (+96/‑68) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 363616 | 59 (0.850) | 10 (0.160) | 8/266 | 7.6 | 25.0% | intergenic (‑134/+33) | lcdH/PP_0303 | L‑carnitine dehydrogenase/dehydrocarnitine cleavage enzyme |
| ? | NC_002947_CJ‑RC | 1499519 = | 6 (0.090) | intergenic (+96/‑68) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5762250 | 29 (0.420) | 4 (0.070) | 4/226 | 8.7 | 18.4% | intergenic (+44/+112) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | = 5762278 | 13 (0.240) | intergenic (+72/+84) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947_CJ‑RC | 478261 = | 24 (0.350) | 4 (0.070) | 4/230 | 8.9 | 20.5% | intergenic (+9/+101) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947_CJ‑RC | 478356 = | 12 (0.220) | intergenic (+104/+6) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 2472140 | 29 (0.420) | 4 (0.080) | 3/212 | 9.0 | 16.6% | intergenic (+44/+105) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | = 2472186 | 19 (0.370) | intergenic (+90/+59) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||