mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 33 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,097,118 | 0 | C | A | 45.0% | 5.3 / 16.0 | 20 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,741,871 | 0 | G | T | 39.8% | 110.1 / 30.5 | 103 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,756,353 | 0 | C | A | 35.6% | 124.4 / 23.9 | 90 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 3,911,533 | 0 | C | A | 35.3% | 181.4 / 22.2 | 119 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,054,894 | 0 | G | T | 33.8% | 102.4 / 18.9 | 74 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,241,875 | 0 | G | T | 33.3% | 140.3 / 11.3 | 84 | P127Q (CCG→CAG) | xylE | D‑xylose:H(+) symporter |
| * | NC_000913 | 1,631,903 | 0 | G | T | 32.3% | 99.9 / 10.4 | 65 | S128Y (TCC→TAC) | ydfJ | putative transporter YdfJ |
| * | NC_000913 | 2,326,713 | 0 | C | A | 31.6% | 129.5 / 10.3 | 76 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 58,065 | 0 | C | A | 31.5% | 116.2 / 10.0 | 73 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 320,845 | 0 | C | A | 31.2% | 103.8 / 13.1 | 77 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 4,406,302 | 0 | C | A | 30.5% | 149.2 / 13.6 | 95 | S38Y (TCC→TAC) | nsrR | DNA‑binding transcriptional regulator NsrR |
| * | NC_000913 | 2,288,418 | 0 | G | T | 30.3% | 240.6 / 21.6 | 122 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 2,990,480 | 0 | C | A | 29.7% | 189.0 / 10.9 | 118 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 180,048 | 0 | C | A | 29.3% | 167.6 / 11.1 | 99 | S271Y (TCC→TAC) | dgt | dGTP triphosphohydrolase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 29.2% | 235.9 / 20.2 | 120 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 1,995,370 | 0 | C | A | 27.9% | 180.5 / 15.7 | 104 | intergenic (‑11/‑285) | uvrY/yecU | DNA‑binding transcriptional activator UvrY/protein YecU |
| * | NC_000913 | 834,674 | 0 | C | A | 27.6% | 136.1 / 12.3 | 76 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 3,451,695 | 0 | C | A | 26.5% | 225.0 / 13.3 | 102 | E198* (GAG→TAG) | rplD | 50S ribosomal subunit protein L4 |
| * | NC_000913 | 847,955 | 0 | G | A | 26.3% | 229.4 / 36.5 | 133 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,032,307 | 0 | C | T | 26.3% | 177.4 / 28.1 | 97 | T314M (ACG→ATG) | uacT | urate:H(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 54 (0.670) | 13 (0.220) | 12/434 | 3.1 | 23.3% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 46 (0.780) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 3648146 | 96 (1.200) | 13 (0.200) | 13/474 | 3.2 | 14.1% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 81 (1.260) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2947467 | 56 (0.700) | 9 (0.160) | 9/424 | 3.9 | 18.0% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 42 (0.730) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2521006 | 63 (0.790) | 7 (0.120) | 7/438 | 4.7 | 14.5% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 36 (0.600) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 1287262 | 73 (0.910) | 10 (0.130) | 9/548 | 5.0 | 15.3% | noncoding (67/85 nt) | tyrV | tRNA‑Tyr |
| ? | NC_000913 | 1287382 = | 43 (0.580) | intergenic (‑54/+156) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 11 (0.140) | 9/590 | 5.4 | 9.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4215399 | 109 (1.360) | intergenic (+190/‑79) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A | |||||
| * | ? | NC_000913 | 4368261 = | 89 (1.110) | 8 (0.100) | 8/588 | 5.7 | 8.4% | coding (67/1437 nt) | aspA | aspartate ammonia‑lyase |
| ? | NC_000913 | = 4368276 | 86 (1.080) | coding (52/1437 nt) | aspA | aspartate ammonia‑lyase | |||||
| * | ? | NC_000913 | 1396044 = | NA (NA) | 11 (0.140) | 8/590 | 5.8 | 9.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1434514 = | 103 (1.280) | intergenic (‑108/+671) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 7 (0.090) | 6/590 | 6.6 | 7.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3262487 | 89 (1.110) | coding (1174/1209 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_000913 | = 1946736 | 75 (0.940) | 6 (0.070) | 6/590 | 6.6 | 7.4% | coding (486/603 nt) | yebB | putative papain‑like amidase YebB |
| ? | NC_000913 | 2068941 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||