Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,922,606 |
A→G |
36.0% |
G872G (GGT→GGC) |
valS ← |
valyl‑tRNA synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,922,606 | 0 | A | G | 36.0%
| 26.0
/ 28.1
| 50 | G872G (GGT→GGC) | valS | valyl‑tRNA synthetase |
| Reads supporting (aligned to +/- strand): ref base A (25/7); new base G (3/15); total (28/22) |
| Fisher's exact test for biased strand distribution p-value = 5.94e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.70e-01 |
TCTTTCGCCAGACGCGCCAGCTCATCTTCTTTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGA > minE/2922538‑2922664
|
tcttTCGCCAGACGCGCCAGCTCATCTTCTTTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCa > 1:3408433/1‑69 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:2486873/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:971165/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:643375/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:3168138/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:3063977/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:236087/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:2360572/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:1988646/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:1540404/68‑1 (MQ=255)
ttCGCCAGACGTGCCAGCTCATCTTCTTTGTTGATGAGGCCTGCCATCGGGATCAGCAGTTCTGCGcc < 1:14071/68‑1 (MQ=255)
tCATCTTCTTTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAAc > 1:350411/1‑68 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCg > 1:3058676/1‑59 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACgg > 1:1818107/1‑65 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:1051516/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:1415255/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:924784/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:914168/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:859560/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:685872/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:666703/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:1069004/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:505767/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:1119377/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:3394954/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:2942721/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:1029694/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:2052751/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAAc > 1:2563691/1‑69 (MQ=255)
ttcttTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTATGCACCGTCGATGATCTTCGTAACGGaaa > 1:759315/1‑68 (MQ=255)
gttgATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGAcc > 1:188537/1‑69 (MQ=255)
gttgATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGAcc > 1:2260632/1‑69 (MQ=255)
gttgATGAGGCCAGCCATAGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGAcc > 1:527183/1‑69 (MQ=255)
ttgATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGa < 1:3035970/66‑1 (MQ=255)
ttgATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGa < 1:1289411/66‑1 (MQ=255)
ctgccaTCGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTatcatc > 1:828199/3‑67 (MQ=255)
ctgccaTCGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTatcatc > 1:2423807/3‑67 (MQ=255)
ctgccaTCGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTatcatc > 1:757306/3‑67 (MQ=255)
cGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTATCATCAgcaggcag < 1:2036910/69‑1 (MQ=255)
cGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTATCATCAgcaggcag < 1:2357994/69‑1 (MQ=255)
cGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTATCATCAgcaggcag < 1:1150533/69‑1 (MQ=255)
cGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTATCATCAgcaggcag < 1:307729/69‑1 (MQ=255)
cGGGATCAGCAGTTCTGCGCCGTCGACGATCTTTGTAACGGAAACCGGACCTTTATCATCAgcaggcag < 1:970384/69‑1 (MQ=255)
tCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAACCCGGACCATTGTCATCGGCAGGCAGCAc > 1:1358558/1‑67 (MQ=255)
tCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCg > 1:1350276/1‑42 (MQ=255)
tCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACg > 1:1929916/1‑68 (MQ=255)
tctGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGa < 1:2345310/64‑1 (MQ=255)
tctGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGa < 1:1991032/64‑1 (MQ=255)
tctGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGa < 1:2200645/64‑1 (MQ=255)
tctGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGa < 1:2838239/64‑1 (MQ=255)
tctGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGa < 1:2708384/64‑1 (MQ=255)
|
TCTTTCGCCAGACGCGCCAGCTCATCTTCTTTGTTGATGAGGCCAGCCATCGGGATCAGCAGCTCTGCACCGTCGATGATCTTCGTAACGGAAACCGGACCTTTGTCATCGGCAGGCAGCACGGTGA > minE/2922538‑2922664
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
