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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.9% | 29.8 / 34.1 | 39 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 282,118 | 0 | A | C | 32.0% | 25.0 / 21.0 | 25 | intergenic (‑135/‑160) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| * | NC_000913 | 475,971 | 0 | C | G | 29.2% | 35.0 / 16.4 | 24 | intergenic (+20/+11) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| * | NC_000913 | 475,972 | 0 | C | G | 29.2% | 34.9 / 18.8 | 24 | intergenic (+21/+10) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| * | NC_000913 | 282,111 | 0 | T | A | 26.7% | 45.8 / 18.0 | 30 | intergenic (‑128/‑167) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| * | NC_000913 | 282,112 | 0 | T | A | 26.7% | 44.6 / 18.2 | 30 | intergenic (‑129/‑166) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| * | NC_000913 | 282,113 | 0 | T | A | 26.7% | 49.6 / 15.2 | 30 | intergenic (‑130/‑165) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| * | NC_000913 | 282,106 | 0 | G | T | 25.8% | 56.7 / 19.2 | 31 | intergenic (‑123/‑172) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| * | NC_000913 | 4,520,500 | 0 | A | . | 23.7% | 155.1 / 46.0 | 59 | intergenic (‑176/+171) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913 | 4,153,434 | 0 | T | G | 23.1% | 53.9 / 13.2 | 26 | intergenic (‑336/+262) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| * | NC_000913 | 4,153,435 | 0 | T | C | 23.1% | 48.6 / 11.0 | 26 | intergenic (‑337/+261) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| * | NC_000913 | 4,520,504 | 1 | . | T | 22.6% | 134.4 / 61.4 | 62 | intergenic (‑180/+167) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913 | 2,947,344 | 0 | G | . | 21.9% | 109.0 / 29.3 | 41 | intergenic (‑166/‑43) | mltA/metZ | membrane‑bound lytic murein transglycosylase A/tRNA‑Met |
| * | NC_000913 | 1,674,171 | 0 | C | . | 21.4% | 74.5 / 17.8 | 28 | coding (259/1035 nt) | tqsA | pheromone AI‑2 transporter |
| * | NC_000913 | 1,985,112 | 0 | C | G | 20.8% | 51.9 / 11.0 | 24 | intergenic (‑43/+27) | araG/araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,552,078 | 0 | G | A | 20.7% | 61.6 / 10.2 | 29 | intergenic (+87/+320) | fdnI/yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 1,552,079 | 0 | C | A | 20.7% | 68.4 / 10.4 | 29 | intergenic (+88/+319) | fdnI/yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 1,674,177 | 0 | G | T | 20.7% | 67.8 / 11.6 | 29 | E89* (GAG→TAG) ‡ | tqsA | pheromone AI‑2 transporter |
| * | NC_000913 | 1,674,178 | 0 | A | C | 20.7% | 56.9 / 14.1 | 29 | E89A (GAG→GCG) ‡ | tqsA | pheromone AI‑2 transporter |
| * | NC_000913 | 4,614,616 | 0 | C | A | 20.0% | 100.0 / 16.6 | 40 | intergenic (+356/+64) | yjjV/yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Marginal new junction evidence (lowest skew 10 of 79 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 585955 = | 42 (1.070) | 7 (0.180) | 7/252 | 3.2 | 14.2% | intergenic (‑322/‑102) | ompT/pauD | DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER |
| ? | NC_000913 | 585977 = | 44 (1.160) | intergenic (‑344/‑80) | ompT/pauD | DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER | |||||
| * | ? | NC_000913 | = 4534139 | 57 (1.460) | 6 (0.170) | 6/240 | 3.4 | 9.3% | intergenic (‑86/+291) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment |
| ? | NC_000913 | = 4534160 | 64 (1.770) | intergenic (‑107/+270) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment | |||||
| * | ? | NC_000913 | 1840631 = | 42 (1.070) | 6 (0.160) | 6/246 | 3.4 | 11.8% | coding (1165/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase |
| ? | NC_000913 | 1840668 = | 50 (1.350) | coding (1202/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase | |||||
| * | ? | NC_000913 | 835510 = | 30 (0.770) | 6 (0.160) | 6/242 | 3.4 | 15.4% | coding (263/963 nt) | ybiB | putative family 3 glycosyltransferase |
| ? | NC_000913 | 835549 = | 38 (1.040) | coding (302/963 nt) | ybiB | putative family 3 glycosyltransferase | |||||
| * | ? | NC_000913 | 746160 = | 33 (0.840) | 6 (0.160) | 6/244 | 3.4 | 15.8% | coding (226/792 nt) | nei | endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase |
| ? | NC_000913 | 746198 = | 33 (0.900) | coding (264/792 nt) | nei | endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 6 (0.160) | 6/246 | 3.4 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 3689302 = | 45 (1.150) | 5 (0.130) | 5/252 | 3.8 | 9.7% | coding (960/1107 nt) | bcsZ | endo‑1,4‑D‑glucanase |
| ? | NC_000913 | 3689326 = | 49 (1.290) | coding (936/1107 nt) | bcsZ | endo‑1,4‑D‑glucanase | |||||
| * | ? | NC_000913 | 2794028 = | NA (NA) | 5 (0.130) | 5/248 | 3.8 | NA | noncoding (1/136 nt) | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | 2794059 = | NA (NA) | noncoding (32/136 nt) | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | = 224374 | NA (NA) | 5 (0.140) | 5/246 | 3.8 | NA | noncoding (604/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 224403 | NA (NA) | noncoding (633/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 3423554 | 39 (1.000) | 5 (0.130) | 5/258 | 3.9 | 11.4% | intergenic (‑12/+26) | rrfF/thrV | 5S ribosomal RNA of rrnD operon/tRNA‑Thr |
| ? | NC_000913 | 4171603 = | NA (NA) | intergenic (+59/‑34) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon | |||||