mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 121 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_012971 | 875,191 | 0 | G | T | 62.5% | 18.2 / 31.3 | 32 | pseudogene (4/1116 nt) | ECD_RS04405 | replication endonuclease |
| * | NC_012971 | 3,483,975 | 0 | C | T | 60.2% | 72.7 / 123.3 | 103 | G800G (GGC→GGT) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,483,977 | 0 | G | A | 60.2% | 84.9 / 121.7 | 103 | W801* (TGG→TAG) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,483,978 | 0 | G | C | 59.8% | 81.2 / 144.4 | 103 | W801C (TGG→TGC) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,483,982 | 0 | T | G | 58.5% | 85.9 / 121.2 | 106 | S803A (TCA→GCA) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,950 | 0 | T | C | 56.7% | 18.3 / 197.2 | 150 | T1125T (ACT→ACC) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,133 | 0 | A | C | 56.4% | 73.0 / 143.3 | 118 | Y853S (TAT→TCT) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,086 | 0 | C | T | 56.2% | 57.9 / 171.3 | 128 | Y837Y (TAC→TAT) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,075 | 0 | T | A | 55.7% | 59.1 / 214.3 | 123 | S834T (TCC→ACC) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,130 | 0 | A | T | 55.4% | 47.5 / 216.3 | 121 | Q852L (CAG→CTG) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,804 | 0 | A | G | 52.6% | 31.2 / 205.0 | 136 | T1077A (ACC→GCC) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,806 | 0 | C | G | 51.9% | 29.5 / 232.3 | 135 | T1077T (ACC→ACG) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,484,234 | 0 | A | G | 50.8% | 7.1 / 200.8 | 128 | S887G (AGC→GGC) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 1,403,415 | 0 | G | A | 47.3% | 13.9 / 263.3 | 169 | R26Q (CGG→CAG) | ECD_RS07135 | YdfR family protein |
| * | NC_012971 | 3,483,028 | 0 | T | A | 46.4% | 32.8 / 233.6 | 125 | L485M (TTG→ATG) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,483,030 | 0 | G | A | 46.4% | 18.6 / 177.6 | 125 | L485L (TTG→TTA) ‡ | rhsB | rhs element protein RhsB |
| * | NC_012971 | 1,403,410 | 0 | G | C | 45.4% | 68.0 / 270.7 | 175 | A24A (GCG→GCC) | ECD_RS07135 | YdfR family protein |
| * | NC_012971 | 1,403,423 | 0 | A | G | 45.1% | 58.4 / 245.2 | 173 | K29E (AAA→GAA) | ECD_RS07135 | YdfR family protein |
| * | NC_012971 | 3,482,990 | 0 | A | G | 44.9% | 37.2 / 165.1 | 128 | N472S (AAC→AGC) | rhsB | rhs element protein RhsB |
| * | NC_012971 | 3,483,093 | 0 | T | C | 44.5% | 44.0 / 165.4 | 119 | T506T (ACT→ACC) | rhsB | rhs element protein RhsB |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_012971 | = 739579 | 58 (0.600) | 13 (0.180) | 11/438 | 4.1 | 21.3% | noncoding (76/76 nt) | ECD_RS03630 | tRNA‑Lys |
| ? | NC_012971 | 740008 = | 53 (0.740) | intergenic (+1/‑132) | ECD_RS03645/ECD_RS03650 | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_012971 | = 739785 | 83 (0.860) | 12 (0.170) | 10/438 | 4.4 | 17.3% | noncoding (76/76 nt) | ECD_RS03640 | tRNA‑Lys |
| ? | NC_012971 | 740008 = | 53 (0.740) | intergenic (+1/‑132) | ECD_RS03645/ECD_RS03650 | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_012971 | = 3510532 | 102 (1.060) | 11 (0.140) | 10/474 | 4.8 | 12.4% | intergenic (‑358/‑382) | dinQ/arsR | damage‑inducible type I toxin DinQ/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
| ? | NC_012971 | 3510764 = | 73 (0.940) | intergenic (‑590/‑150) | dinQ/arsR | damage‑inducible type I toxin DinQ/As(III)‑sensing metalloregulatory transcriptional repressor ArsR | |||||
| * | ? | NC_012971 | = 739290 | 99 (1.030) | 6 (0.080) | 6/438 | 5.9 | 9.4% | noncoding (76/76 nt) | ECD_RS03620 | tRNA‑Lys |
| ? | NC_012971 | 739580 = | 42 (0.590) | intergenic (+1/‑51) | ECD_RS03630/ECD_RS03635 | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_012971 | = 656615 | 67 (0.700) | 8 (0.110) | 6/434 | 5.9 | 13.8% | intergenic (‑1/+15) | ECD_RS03205/ECD_RS03210 | tRNA‑Met/tRNA‑Gln |
| ? | NC_012971 | 657008 = | 51 (0.720) | intergenic (‑2/+379) | ECD_RS03225/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NC_012971 | = 3643247 | 112 (1.160) | 10 (0.110) | 8/534 | 6.1 | 9.0% | coding (1822/4851 nt) | ECD_RS18090 | YadA‑like family protein |
| ? | NC_012971 | 3643503 = | 102 (1.170) | coding (2078/4851 nt) | ECD_RS18090 | YadA‑like family protein | |||||
| * | ? | NC_012971 | = 930604 | 63 (0.650) | 5 (0.060) | 5/472 | 6.8 | 9.5% | noncoding (118/136 nt) | ECD_RS22710 | RtT sRNA |
| ? | NC_012971 | 930960 = | 45 (0.580) | noncoding (69/88 nt) | ECD_RS04720 | tRNA‑Ser | |||||
| * | ? | NC_012971 | = 656380 | 75 (0.780) | 6 (0.070) +45 bp |
5/500 | 7.1 | 8.5% | intergenic (‑2/+36) | ECD_RS03195/ECD_RS03200 | tRNA‑Gln/tRNA‑Gln |
| ? | NC_012971 | 656930 = | 77 (0.800) | noncoding (77/77 nt) | ECD_RS03225 | tRNA‑Met | |||||
| * | ? | NC_012971 | = 2517850 | 0 (0.000) | 9 (0.090) +TT |
6/586 | 7.5 | 16.3% | intergenic (+31/‑53) | sseA/ECD_RS25300 | 3‑mercaptopyruvate sulfurtransferase/IS3‑like element ISEcB1 family transposase |
| ? | NC_012971 | 2519624 = | 93 (0.970) | intergenic (+364/‑302) | ECD_RS25300/timP | IS3‑like element ISEcB1 family transposase/small toxic inner membrane protein TimP | |||||
| * | ? | NC_012971 | 739932 = | 85 (0.880) | 6 (0.060) +GG |
6/586 | 7.5 | 6.8% | noncoding (1/76 nt) | ECD_RS03645 | tRNA‑Lys |
| ? | NC_012971 | = 2397543 | 80 (0.830) | noncoding (76/76 nt) | ECD_RS11975 | tRNA‑Val | |||||