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 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,808,403 |
2 bp→AA |
100% |
coding (116‑117/714 nt) |
aphA → |
acid phosphatase/phosphotransferase, class B, non‑specific |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,808,403 | 0 | G | A | 82.0%
| 158.9
/ 27.0
| 72 | R39K (AGG→AAA) | aphA | acid phosphatase/phosphotransferase, class B, non‑specific |
| Reads supporting (aligned to +/- strand): ref base G (0/13); new base A (0/59); total (0/72) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 2,808,404 | 0 | G | A | 82.0%
| 158.5
/ 26.5
| 72 | R39K (AGG→AAA) | aphA | acid phosphatase/phosphotransferase, class B, non‑specific |
| Reads supporting (aligned to +/- strand): ref base G (0/13); new base A (0/59); total (0/72) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GACTAACGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGCACAAATTGAAAATA > minE/2808389‑2808456
||
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:265364/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1797175/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:180968/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1832334/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1870420/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1884045/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1905335/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1919809/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2174043/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2202073/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2209312/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2264585/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2286489/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2313763/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:237574/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:261146/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1048027/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:278358/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:279510/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:296586/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:435684/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:454221/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:504947/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:515341/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:544945/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:743750/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:785996/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:816753/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:821222/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:884552/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:889742/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:995330/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:175209/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1038598/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1054830/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1076657/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1102606/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:118961/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1195365/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1243706/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1390706/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1401972/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1417040/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1465559/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1499844/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1531306/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1677033/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1545496/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1567853/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1763624/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1605753/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1539415/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1576845/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1578344/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1702201/59‑1 (MQ=255)
taCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1679391/59‑1 (MQ=255)
aCTAACGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGCACAAATTGAAAATa < 1:1351551/67‑1 (MQ=255)
aCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:1220274/59‑1 (MQ=255)
aCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:839018/59‑1 (MQ=255)
aCTAACGTAGCCAAACTCGCTGAACAGGCGCCAATTCATTGGGTTTCGGTTGCACAAAt < 1:2181400/59‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:174191/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:998089/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1899496/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1247030/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1229717/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:53321/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:40800/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:299726/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1446646/50‑1 (MQ=255)
aCGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:2238948/50‑1 (MQ=255)
cGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1339108/49‑1 (MQ=255)
cGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGca < 1:1426486/49‑1 (MQ=255)
||
GACTAACGTTGCCAGGCTTGCTGAACAGGCACCCATTCATTGGGTTTCGGTCGCACAAATTGAAAATA > minE/2808389‑2808456
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
