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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,166,849 | 0 | G | A | 61.0% | 2.1 / 42.3 | 41 | noncoding (191/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 3,054,886 | 0 | G | T | 39.3% | 118.9 / 35.1 | 89 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,288,418 | 0 | G | T | 35.9% | 152.3 / 13.1 | 92 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.9% | 108.8 / 22.8 | 84 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,631,903 | 0 | G | T | 34.7% | 100.9 / 15.5 | 75 | S128Y (TCC→TAC) | ydfJ | putative transporter YdfJ |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.2% | 183.1 / 14.3 | 120 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,902,613 | 0 | C | A | 33.8% | 107.9 / 19.3 | 72 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 847,955 | 0 | G | A | 31.9% | 162.4 / 45.2 | 113 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,032,307 | 0 | C | T | 31.8% | 140.5 / 30.2 | 88 | T314M (ACG→ATG) | uacT | urate:H(+) symporter |
| * | NC_000913 | 1,922,815 | 0 | C | A | 30.1% | 188.9 / 12.7 | 103 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 228,689 | 0 | T | . | 29.1% | 201.9 / 134.9 | 111 | intergenic (+27/‑67) | rrlH/rrfH | 23S ribosomal RNA/5S ribosomal RNA |
| * | NC_000913 | 1,286,793 | 0 | A | G | 28.6% | 90.6 / 43.9 | 56 | K29E (AAG→GAG) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 3,623,538 | 0 | G | A | 28.1% | 158.2 / 16.2 | 96 | G47D (GGT→GAT) | yhhH | PF15631 family protein YhhH |
| * | NC_000913 | 1,502,770 | 0 | T | C | 27.4% | 170.4 / 18.0 | 95 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 2,490,240 | 0 | G | T | 26.7% | 192.2 / 12.1 | 105 | intergenic (‑54/+16) | yfdV/oxc | putative transport protein YfdV/oxalyl‑CoA decarboxylase |
| * | NC_000913 | 1,334,966 | 0 | A | C | 25.6% | 204.0 / 13.9 | 129 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,431,396 | 0 | C | A | 25.6% | 265.2 / 12.0 | 130 | R7I (AGA→ATA) | tsaC | L‑threonylcarbamoyladenylate synthase |
| * | NC_000913 | 1,286,831 | 0 | T | A | 24.6% | 110.5 / 43.3 | 60 | A41A (GCT→GCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 1,286,870 | 0 | C | A | 23.6% | 103.2 / 18.8 | 55 | S54S (TCC→TCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 1,502,772 | 0 | G | A | 23.2% | 173.6 / 18.1 | 95 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 64 (0.780) | 10 (0.170) | 8/434 | 4.2 | 17.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 49 (0.810) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2518116 | 75 (0.910) | 8 (0.130) | 6/428 | 4.9 | 13.6% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 47 (0.790) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 2653419 | 58 (0.710) | 6 (0.080) | 6/540 | 6.0 | 8.1% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 83 (1.110) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4094319 | 71 (0.870) | 6 (0.070) +C |
6/588 | 6.4 | 8.2% | intergenic (‑47/+404) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094689 = | 63 (0.770) | intergenic (‑417/+34) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 2878076 | 31 (0.380) | 7 (0.090) +T |
6/588 | 6.4 | 11.9% | intergenic (+458/+493) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| ? | NC_000913 | 2878324 = | 73 (0.890) | intergenic (+706/+245) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 | |||||
| * | ? | NC_000913 | = 2653393 | 62 (0.760) | 6 (0.070) | 6/584 | 6.4 | 7.1% | noncoding (63/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653720 = | 95 (1.170) | intergenic (‑265/‑135) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 1287248 | 84 (1.020) | 6 (0.070) +A |
6/588 | 6.4 | 8.1% | noncoding (81/85 nt) | tyrV | tRNA‑Tyr |
| ? | NC_000913 | 1287544 = | 53 (0.650) | noncoding (79/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1286906 | 49 (0.600) | 8 (0.100) | 4/550 | 7.1 | 15.0% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 45 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1166125 | 89 (1.080) | 5 (0.060) | 4/560 | 7.2 | 6.1% | coding (41/1305 nt) | ndh | NADH:quinone oxidoreductase II |
| ? | NC_000913 | 1166621 = | 69 (0.890) | coding (537/1305 nt) | ndh | NADH:quinone oxidoreductase II | |||||
| * | ? | NC_000913 | = 1069777 | 63 (0.770) | 4 (0.050) | 4/574 | 7.3 | 6.5% | coding (63/1329 nt) | rutG | pyrimidine:H(+) symporter |
| ? | NC_000913 | 1070265 = | 53 (0.660) | coding (90/495 nt) | rutF | FMN reductase RutF | |||||