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 41 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 | 2 | . | A | 70.6% | 67.1 / 31.7 | 34 | 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 | 66.7% | 59.8 / 31.3 | 34 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.0% | 54.0 / 229.0 | 153 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.5% | ‑2.8 / 136.4 | 97 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 47.7% | 38.8 / 156.6 | 109 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 47.2% | 27.2 / 115.2 | 92 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,844,599 | 0 | C | . | 46.2% | 20.4 / 18.3 | 13 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 42.9% | 18.7 / 41.6 | 28 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 4,844,607 | 1 | . | G | 42.9% | ‑5.4 / 27.6 | 14 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,248 | 0 | A | T | 40.6% | 27.6 / 33.6 | 32 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 40.0% | 30.4 / 40.4 | 31 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 39.1% | 14.5 / 12.0 | 23 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 38.7% | 36.0 / 32.5 | 31 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 38.6% | 39.4 / 10.9 | 51 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 37.0% | 40.7 / 11.9 | 50 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 36.2% | 68.9 / 11.8 | 50 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 35.9% | 33.3 / 11.2 | 39 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 74,484 | 0 | G | T | 30.8% | 77.0 / 12.6 | 39 | intergenic (+72/+26) | PP_0063/PP_0064 | lipid A biosynthesis lauroyl acyltransferase/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,013,234 | 0 | C | A | 30.8% | 49.4 / 18.7 | 26 | intergenic (+62/+69) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 284,586 | 0 | T | A | 30.0% | 10.5 / 12.8 | 22 | intergenic (+33/+30) | betT‑II/atsK | choline/carnitine/betaine transporter/alpha‑ketoglutarate‑dependent sulfonate dioxygenase |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 66 (0.940) | 19 (0.320) | 13/250 | 5.2 | 39.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.100) | 15 (0.280) | 10/220 | 5.5 | 52.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 22 (0.410) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.070) | 17 (0.260) | 12/266 | 6.0 | 38.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 50 (0.780) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 38 (0.540) | 12 (0.180) | 12/280 | 6.3 | 20.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 56 (0.830) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 15 (0.210) | 14 (0.220) | 11/268 | 6.4 | 44.5% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 21 (0.320) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.070) | 10 (0.170) | 7/250 | 7.7 | 36.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 31 (0.510) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 10 (0.150) +GCC |
8/284 | 8.1 | 91.1% | 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 | 1499507 = | 3 (0.040) | 7 (0.110) | 6/266 | 8.7 | 17.8% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 62 (0.970) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 54 (0.770) | 6 (0.090) | 6/274 | 8.9 | 12.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 30 (0.450) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1487035 | 21 (0.300) | 4 (0.070) | 4/230 | 8.9 | 21.2% | intergenic (+51/+79) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | = 1487065 | 13 (0.230) | intergenic (+81/+49) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||