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 |
2,801,283:1 |
+G |
100% |
coding (741/1038 nt) |
yjbN → |
tRNA‑dihydrouridine synthase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,801,283 | 1 | . | G | 79.1%
| 130.1
/ 26.9
| 43 | coding (741/1038 nt) | yjbN | tRNA‑dihydrouridine synthase A |
| Reads supporting (aligned to +/- strand): ref base . (0/9); new base G (0/34); total (0/43) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGT > minE/2801233‑2801324
|
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:253152/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:130580/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:768433/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:746222/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:386716/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:1458624/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:1743503/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:542677/67‑1 (MQ=255)
tCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATc < 1:444798/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGcggcggc < 1:59525/67‑2 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:350998/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:852726/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:393672/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:398906/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:406947/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:439247/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:511405/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:549015/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:566570/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:606718/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:664083/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:729202/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:79217/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1016918/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1904987/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1135744/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1178160/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1338882/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1357539/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1357609/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1444392/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1480105/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1607617/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1692806/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:323302/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:2003234/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:2026882/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:206069/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:2070748/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:2091840/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:244529/67‑1 (MQ=255)
gCAACATATGGATGGCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:307220/67‑1 (MQ=255)
gCGTGATGGTCGGGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGt < 1:1924712/53‑1 (MQ=255)
c‑GGGCGCGAGGCGTATCAGAATCCGGGTATTCTGgcggcg > 1:1912548/1‑40 (MQ=255)
|
TCGCTGGAAGAGGCCAAAGCACACCTGCAACATATGGATGGCGTGATGGTC‑GGGCGCGAGGCGTATCAGAATCCGGGTATTCTGGCGGCGGT > minE/2801233‑2801324
|
| 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
