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 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,145,674:1 |
+CAA |
100% |
coding (1033/1626 nt) |
yhbX ← |
predicted hydrolase, inner membrane |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,145,674 | 1 | . | C | 77.6%
| 144.8
/ 35.8
| 49 | coding (1033/1626 nt) | yhbX | predicted hydrolase, inner membrane |
| Reads supporting (aligned to +/- strand): ref base . (1/10); new base C (38/0); total (39/10) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-09 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.54e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 2,145,674 | 2 | . | A | 77.6%
| 128.8
/ 35.9
| 49 | coding (1033/1626 nt) | yhbX | predicted hydrolase, inner membrane |
| Reads supporting (aligned to +/- strand): ref base . (1/10); new base A (38/0); total (39/10) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-09 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 2,145,674 | 3 | . | A | 77.6%
| 132.3
/ 35.9
| 49 | coding (1033/1626 nt) | yhbX | predicted hydrolase, inner membrane |
| Reads supporting (aligned to +/- strand): ref base . (1/10); new base A (38/0); total (39/10) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-09 |
| 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. |
AGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGGCGCGC > minE/2145628‑2145723
|||
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcttca < 1:398163/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:1181830/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:886882/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:7258/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:270016/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:2096878/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:1871657/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:1843251/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:1429108/63‑1 (MQ=255)
aGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATtcatca < 1:1228608/63‑1 (MQ=255)
gCTTGCGATAAATGCCAA‑‑‑CAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcgcgc > 1:1008367/1‑67 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCct > 1:75470/1‑42 (MQ=25)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:732187/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:428505/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:432342/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:439641/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:451861/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:512699/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:66274/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:682252/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:695594/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:381624/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:815887/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:828009/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:832759/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:862001/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:891768/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:942999/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:965798/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1354510/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:142976/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1494807/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1513896/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1519980/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:163680/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1644975/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1671734/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:176824/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1795343/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1251529/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1275878/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:2031625/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:2032806/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:2068783/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:208732/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1268628/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:2123944/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:1265500/1‑66 (MQ=255)
gCTTGCGATAAATG‑CGGCAACAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGgcg > 1:381370/1‑66 (MQ=255)
|||
AGTTTCTTTTGCTGCGTATTTTGCTGTAATGCTTGCGATAAATG‑CGG‑‑‑CAACAACAATTCATCAAATCCTCTGACATAAACTGTTTCCATGGCGCGC > minE/2145628‑2145723
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
