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 |
2,349,130 |
C→T |
100% |
E840K (GAA→AAA) |
polA ← |
fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,349,130 | 0 | C | T | 85.7%
| 52.8
/ 2.8
| 21 | E840K (GAA→AAA) | polA | fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
| Reads supporting (aligned to +/- strand): ref base C (0/3); new base T (0/18); total (0/21) |
| 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. |
AATGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTCAGCCGCTGCACGACGAGCACCATTGCTGGATTTGATATCCGGCAGATA > minE/2349083‑2349178
|
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:2091923/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:872881/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:686597/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:620764/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:513664/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:504060/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:463996/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:443508/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:31519/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:2156730/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:1086356/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:2080470/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:1220302/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:1159928/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:1146088/66‑1 (MQ=255)
aaTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCAAGTTTAGCCGCTGCACGACGAGc < 1:2056251/66‑1 (MQ=255)
aTGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:1264845/65‑1 (MQ=255)
gCATTGGCGCGTTAATGGCTGCACGTTTAGCCGCTGCACGACGAGc < 1:695229/46‑1 (MQ=255)
cgTTAATGGCTGCACGTTCAGCCGCTGCACGACGAGCACCATTGCTGGATTTGATATCCGGCAGATa < 1:1706965/67‑1 (MQ=255)
cgTTAATGGCTGCACGTTCAGCCGCTGCACGACGAGCACCATTGCTGGATTTGATATCCGGCAGATa < 1:1662822/67‑1 (MQ=255)
cgTTAATGGCTGCACGTTCAGCCGCTGCACGACGAGCACCATTGCTGGATTTGATATCCGGCAGATa < 1:127145/67‑1 (MQ=255)
|
AATGTCGGCGGCGGTTCCCTGCATTGGCGCGTTAATGGCTGCACGTTCAGCCGCTGCACGACGAGCACCATTGCTGGATTTGATATCCGGCAGATA > minE/2349083‑2349178
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
