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 | 70.3% | 33.5 / 46.9 | 68 | V173A (GTT→GCT) | LY180_07445 | transposase IS609 |
| * | CP006584 | 1,643,582 | 0 | G | A | 65.8% | 262.6 / 225.7 | 242 | intergenic (‑242/‑61) | LY180_07760/LY180_07765 | sulfatase/transposase |
| * | CP006584 | 3,850,024 | 0 | C | T | 62.6% | 137.8 / 186.2 | 182 | P363S (CCA→TCA) | LY180_18350 | transcriptional regulator |
| * | CP006584 | 269,452 | 0 | C | T | 51.2% | 12.4 / 280.7 | 205 | Q60* (CAA→TAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,400 | 0 | G | A | 50.8% | 12.8 / 262.6 | 188 | E42E (GAG→GAA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,443 | 0 | T | G | 50.0% | 8.6 / 295.9 | 201 | F57V (TTT→GTT) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,116 | 0 | C | T | 49.4% | 3.4 / 249.4 | 175 | R121R (CGC→CGT) | LY180_01180 | hypothetical protein |
| * | CP006584 | 269,453 | 0 | A | G | 49.2% | 9.4 / 297.1 | 205 | Q60R (CAA→CGA) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,438 | 0 | T | C | 49.0% | 2.5 / 286.7 | 199 | L55P (CTC→CCC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,403 | 0 | T | C | 48.6% | 6.9 / 270.0 | 191 | G43G (GGT→GGC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 269,492 | 0 | C | T | 46.5% | 60.7 / 252.7 | 202 | T73I (ACC→ATC) | LY180_01185 | hypothetical protein |
| * | CP006584 | 3,513,965 | 0 | T | C | 44.4% | 19.9 / 84.5 | 72 | intergenic (‑141/+198) | tldD/LY180_16725 | protease TldD/membrane protein |
| * | CP006584 | 269,041 | 0 | T | C | 43.0% | 42.3 / 188.9 | 157 | D96D (GAT→GAC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 269,044 | 0 | T | C | 42.7% | 50.1 / 185.5 | 157 | C97C (TGT→TGC) | LY180_01180 | hypothetical protein |
| * | CP006584 | 4,253,976 | 0 | T | A | 39.7% | 201.0 / 294.2 | 230 | F12Y (TTC→TAC) | LY180_20340 | hypothetical protein |
| * | CP006584 | 4,253,902 | 0 | C | T | 37.7% | 208.5 / 215.8 | 215 | intergenic (+24/‑40) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 1,310,833 | 0 | A | G | 36.2% | 120.5 / 123.2 | 129 | intergenic (‑289/+140) | LY180_06180/LY180_06185 | hypothetical protein/hypothetical protein |
| * | CP006584 | 1,563,136 | 0 | T | C | 36.0% | 16.5 / 18.3 | 27 | N139N (AAT→AAC) | LY180_07445 | transposase IS609 |
| * | CP006584 | 4,253,879 | 0 | G | A | 34.8% | 242.8 / 183.9 | 202 | intergenic (+1/‑63) | LY180_20335/LY180_20340 | hypothetical protein/hypothetical protein |
| * | CP006584 | 4,254,025 | 0 | G | A | 34.6% | 240.3 / 191.6 | 214 | A28A (GCG→GCA) | LY180_20340 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006584 | 2253821 = | 75 (0.730) | 26 (0.270) | 25/556 | 4.0 | 30.2% | coding (38/414 nt) | LY180_10760 | hypothetical protein |
| ? | CP006584 | 2255662 = | 49 (0.500) | coding (826/1284 nt) | LY180_10775 | tail protein | |||||
| * | ? | CP006584 | = 4739815 | 123 (1.200) | 22 (0.220) | 20/568 | 5.1 | 15.1% | intergenic (+56/‑424) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A |
| ? | CP006584 | = 4740111 | 129 (1.290) | intergenic (+352/‑128) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A | |||||
| * | ? | CP006584 | 4739807 = | 120 (1.170) | 18 (0.180) | 18/568 | 5.5 | 12.8% | intergenic (+48/‑432) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A |
| ? | CP006584 | 4740121 = | 130 (1.300) | intergenic (+362/‑118) | LY180_22625/fimA | tyrosine recombinase/type‑1 fimbrial protein subunit A | |||||
| * | ? | CP006584 | = 2253835 | 69 (0.670) | 16 (0.160) | 16/556 | 5.9 | 21.9% | coding (52/414 nt) | LY180_10760 | hypothetical protein |
| ? | CP006584 | = 2255646 | 49 (0.500) | coding (842/1284 nt) | LY180_10775 | tail protein | |||||
| * | ? | CP006584 | 3513986 = | 71 (0.690) | 22 (0.320) +99 bp |
3/388 | 9.0 | 32.8% | intergenic (‑162/+177) | tldD/LY180_16725 | protease TldD/membrane protein |
| ? | CP006584 | = 3514068 | 65 (0.630) | intergenic (‑244/+95) | tldD/LY180_16725 | protease TldD/membrane protein | |||||
| * | ? | CP006584 | = 1682216 | 123 (1.200) | 5 (0.050) | 5/586 | 10.2 | 3.9% | coding (1262/1284 nt) | LY180_07925 | hypothetical protein |
| ? | CP006584 | 1685397 = | NA (NA) | coding (774/1209 nt) | LY180_07935 | hypothetical protein | |||||
| * | ? | CP006584 | 3513901 = | 63 (0.610) | 44 (0.450) +TCGGATAAGGCGTTT |
3/556 | 11.1 | 43.2% | intergenic (‑77/+262) | tldD/LY180_16725 | protease TldD/membrane protein |
| ? | CP006584 | = 3514068 | 59 (0.570) | intergenic (‑244/+95) | tldD/LY180_16725 | protease TldD/membrane protein | |||||
| * | ? | CP006584 | 4214142 = | 132 (1.280) | 3 (0.030) | 3/582 | 11.3 | 2.2% | coding (1217/1242 nt) | LY180_20105 | sugar isomerase |
| ? | CP006584 | 4214159 = | 134 (1.310) | coding (1200/1242 nt) | LY180_20105 | sugar isomerase | |||||
| * | ? | CP006584 | = 4190701 | 111 (1.080) | 3 (0.030) | 3/584 | 11.3 | 2.3% | coding (129/2787 nt) | LY180_20020 | DNA polymerase I |
| ? | CP006584 | = 4547846 | 139 (1.360) | coding (1798/2148 nt) | LY180_21700 | lysine decarboxylase CadA | |||||
| * | ? | CP006584 | 3419664 = | 135 (1.310) | 3 (0.030) | 3/576 | 11.3 | 2.2% | coding (2006/2517 nt) | LY180_16245 | membrane protein |
| ? | CP006584 | 3419690 = | 133 (1.320) | coding (2032/2517 nt) | LY180_16245 | membrane protein | |||||