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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 56.5% | ‑4.0 / 18.5 | 26 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 56.5% | 8.0 / 28.3 | 26 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,905,987 | 0 | G | T | 56.2% | 8.4 / 17.5 | 16 | intergenic (‑136/‑132) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 56.0% | 2.7 / 22.5 | 25 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.5% | 12.1 / 157.9 | 118 | 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 | 50.4% | 56.1 / 212.0 | 140 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 49.1% | 5.1 / 172.2 | 118 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 39.2% | 31.7 / 17.6 | 53 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 38.0% | 37.3 / 14.7 | 51 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 37.5% | 58.7 / 18.8 | 49 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 36.1% | 54.0 / 10.6 | 36 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,211,931 | 0 | A | G | 35.7% | 30.9 / 11.2 | 30 | intergenic (‑94/+84) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 33.3% | 41.0 / 12.1 | 54 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,171,517 | 0 | C | A | 30.2% | 146.9 / 11.1 | 64 | intergenic (+52/+351) | PP_5484/PP_1924 | hypothetical protein/phosphinothricin N‑acetyltransferase |
| * | NC_002947_CJ‑RC | 697,123 | 0 | G | T | 29.0% | 55.5 / 10.5 | 31 | intergenic (+50/‑701) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,505,989 | 0 | T | G | 25.8% | 129.3 / 19.9 | 66 | intergenic (‑348/+133) | PP_3103/PP_5574 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,648,338 | 0 | A | C | 24.0% | 94.2 / 12.2 | 50 | V303G (GTG→GGG) | PP_4112 | sulfate transporter |
| * | NC_002947_CJ‑RC | 4,122,032 | 0 | C | A | 22.4% | 192.2 / 13.6 | 67 | G202C (GGC→TGC) | PP_3625 | LysE family transporter |
| * | NC_002947_CJ‑RC | 2,866,841 | 0 | C | G | 21.2% | 163.7 / 12.2 | 66 | intergenic (‑65/‑1504) | glllA/PP_2520 | gallate dioxygenase/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,175,524 | 0 | C | A | 21.1% | 191.9 / 11.2 | 77 | Q69K (CAA→AAA) | PP_3676 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 23 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 43 (0.550) | 16 (0.210) | 15/282 | 6.0 | 27.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 43 (0.570) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.080) | 10 (0.170) | 8/222 | 7.0 | 31.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.660) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 13 (0.170) +GCC |
11/286 | 7.5 | 86.9% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.030) | 11 (0.140) +CGGG |
10/284 | 7.9 | 85.0% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.030) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 12 (0.150) | 9 (0.120) | 9/278 | 8.2 | 40.5% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 15 (0.200) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 51 (0.650) | 6 (0.080) | 6/276 | 9.7 | 10.8% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 51 (0.690) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 37 (0.470) | 5 (0.070) | 5/278 | 10.3 | 10.2% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 53 (0.710) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 4982286 | 5 (0.060) | 8 (0.100) +GGG |
5/282 | 10.4 | 61.9% | intergenic (‑22/+46) | PP_4387/flgE | hypothetical protein/flagellar hook protein FlgE |
| ? | NC_002947_CJ‑RC | 4982287 = | 5 (0.060) | intergenic (‑23/+45) | PP_4387/flgE | hypothetical protein/flagellar hook protein FlgE | |||||
| * | ? | NC_002947_CJ‑RC | = 1311718 | 27 (0.350) | 5 (0.070) | 5/282 | 10.4 | 15.1% | intergenic (‑186/+92) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA |
| ? | NC_002947_CJ‑RC | 1311803 = | 30 (0.400) | intergenic (‑271/+7) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA | |||||
| * | ? | NC_002947_CJ‑RC | 2478409 = | 7 (0.090) | 3 (0.050) | 3/240 | 10.6 | 43.6% | coding (106/444 nt) | PP_2172 | hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2478405 | 2 (0.030) | coding (102/444 nt) | PP_2172 | hypothetical protein | |||||