mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006584 | 1,563,237 | 0 | T | C | 72.5% | 29.9 / 24.5 | 41 | V173A (GTT→GCT) | LY180_07445 | transposase IS609 |
| * | CP006584 | 1,643,582 | 0 | G | A | 61.3% | 93.5 / 125.5 | 127 | intergenic (‑242/‑61) | LY180_07760/LY180_07765 | sulfatase/transposase |
| * | CP006584 | 3,513,965 | 0 | T | C | 48.9% | 0.8 / 63.4 | 47 | intergenic (‑141/+198) | tldD/LY180_16725 | protease TldD/membrane protein |
| * | CP006584 | 269,116 | 0 | C | T | 45.2% | 24.5 / 102.3 | 87 | R121R (CGC→CGT) | LY180_01180 | hypothetical protein |
| * | CP006584 | 269,438 | 0 | T | C | 36.8% | 92.9 / 112.1 | 118 | L55P (CTC→CCC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 4,253,902 | 0 | C | T | 36.1% | 134.5 / 112.3 | 124 | intergenic (+24/‑40) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 269,400 | 0 | G | A | 36.0% | 107.9 / 98.9 | 112 | E42E (GAG→GAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 1,310,832 | 0 | T | G | 35.7% | 63.2 / 76.7 | 70 | intergenic (‑288/+141) | LY180_06180/LY180_06185 | hypothetical protein/hypothetical protein |
| * | CP006584 | 269,443 | 0 | T | G | 35.5% | 85.2 / 142.4 | 121 | F57V (TTT→GTT) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,452 | 0 | C | T | 35.5% | 120.8 / 112.4 | 122 | Q60* (CAA→TAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,453 | 0 | A | G | 35.2% | 105.4 / 121.8 | 122 | Q60R (CAA→CGA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,403 | 0 | T | C | 33.9% | 103.5 / 105.3 | 113 | G43G (GGT→GGC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 1,310,833 | 0 | A | G | 33.8% | 70.2 / 60.5 | 69 | intergenic (‑289/+140) | LY180_06180/LY180_06185 | hypothetical protein/hypothetical protein |
| * | CP006584 | 4,253,976 | 0 | T | A | 33.1% | 151.3 / 135.0 | 133 | F12Y (TTC→TAC) | LY180_20340 | hypothetical protein |
| * | CP006584 | 269,492 | 0 | C | T | 32.2% | 133.0 / 93.7 | 121 | T73I (ACC→ATC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,041 | 0 | T | C | 32.1% | 88.9 / 65.4 | 84 | D96D (GAT→GAC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 269,044 | 0 | T | C | 31.3% | 88.6 / 65.3 | 84 | C97C (TGT→TGC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 1,643,618 | 0 | C | G | 30.5% | 186.7 / 123.6 | 132 | intergenic (‑278/‑25) | LY180_07760/LY180_07765 | sulfatase/transposase |
| * | CP006584 | 4,253,879 | 0 | G | A | 30.5% | 176.6 / 90.7 | 119 | intergenic (+1/‑63) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 4,254,025 | 0 | G | A | 29.5% | 184.7 / 93.4 | 132 | A28A (GCG→GCA) | LY180_20340 | hypothetical protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006584 | 2253821 = | 30 (0.490) | 14 (0.240) | 12/558 | 3.4 | 34.8% | coding (38/414 nt) | LY180_10760 | hypothetical protein |
| ? | CP006584 | 2255662 = | 24 (0.410) | coding (826/1284 nt) | LY180_10775 | tail protein | |||||
| * | ? | CP006584 | 4739807 = | 67 (1.100) | 8 (0.140) | 8/570 | 4.4 | 10.3% | intergenic (+48/‑432) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A |
| ? | CP006584 | 4740121 = | 74 (1.250) | intergenic (+362/‑118) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A | |||||
| * | ? | CP006584 | = 1213484 | 0 (0.000) | 8 (0.130) | 8/588 | 4.6 | 100% | intergenic (+183/‑112) | LY180_05705/LY180_05710 | DNAse/PTS glucose transporter subunit IIBC |
| ? | CP006584 | 1213492 = | 0 (0.000) | intergenic (+191/‑104) | LY180_05705/LY180_05710 | DNAse/PTS glucose transporter subunit IIBC | |||||
| * | ? | CP006584 | = 3884875 | 120 (1.960) | 6 (0.100) | 6/586 | 5.2 | 5.0% | coding (905/1137 nt) | LY180_18515 | membrane protein |
| ? | CP006584 | 3885089 = | 108 (1.770) | coding (691/1137 nt) | LY180_18515 | membrane protein | |||||
| * | ? | CP006584 | 794676 = | NA (NA) | 7 (0.120) | 6/578 | 5.2 | NA | coding (1871/4200 nt) | LY180_03720 | rhsA |
| ? | CP006584 | = 794771 | NA (NA) | coding (1966/4200 nt) | LY180_03720 | rhsA | |||||
| * | ? | CP006584 | = 4400614 | NA (NA) | 4 (0.070) | 3/586 | 6.5 | 5.0% | intergenic (+871/‑175) | LY180_21040/LY180_21045 | hypothetical protein/5S ribosomal RNA |
| ? | CP006584 | = 4416210 | 77 (1.260) | coding (663/690 nt) | LY180_21095 | (alpha)‑aspartyl dipeptidase | |||||
| * | ? | CP006584 | 2786005 = | 53 (0.870) | 3 (0.050) | 3/588 | 6.5 | 4.0% | coding (449/1623 nt) | LY180_13205 | L‑aspartate oxidase |
| ? | CP006584 | = 3928372 | 92 (1.510) | intergenic (‑290/‑123) | LY180_18705/LY180_18710 | lipopolysaccharide core heptosyltransferase RfaQ/3‑deoxy‑D‑manno‑octulosonic acid transferase | |||||
| * | ? | CP006584 | = 497934 | 59 (0.970) | 3 (0.050) | 3/578 | 6.5 | 4.8% | coding (719/1848 nt) | secD | preprotein translocase subunit SecD |
| ? | CP006584 | = 497954 | 60 (1.000) | coding (739/1848 nt) | secD | preprotein translocase subunit SecD | |||||