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 |
2,284,209 |
C→T |
100% |
Q443Q (CAG→CAA) |
argH ← |
argininosuccinate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,284,209 | 0 | C | T | 87.7%
| 26.2
/ ‑3.0
| 16 | Q443Q (CAG→CAA) | argH | argininosuccinate lyase |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (14/0); total (15/1) |
| Fisher's exact test for biased strand distribution p-value = 1.25e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTTACCCTAACCGAGCCTGCGCAAAAGCAATCGCCTGCGCCACCTGCTGCGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGA > minE/2284163‑2284276
|
cTTACCCTAACCGAGCCTGCGCAAAAGCAATCGCCTGCGCCACCTGCTGCGGTGAGACGCCGCCTTTTg > 1:254833/1‑69 (MQ=255)
cAAAAGCAATCGCCTGCGCCACCTGCTGCGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCAc < 1:2862930/68‑1 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCatc > 1:991879/1‑67 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAg > 1:2677004/1‑68 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:996162/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:461595/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:279426/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:2784131/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:2570746/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:252197/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:1464303/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:2130950/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:208357/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:1937347/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:189527/1‑69 (MQ=255)
aTCGCCTGCGCCACCTGTTGCGGTGAGACACCGCCTTTTGCTGCACGCTTGTCGAGGCACGATTGCAGc > 1:1686583/1‑69 (MQ=255)
tgctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAg < 1:1033463/69‑1 (MQ=255)
tgctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAg < 1:3200474/69‑1 (MQ=255)
tgctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAg < 1:657041/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATa > 1:532664/1‑67 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:3207839/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa < 1:991316/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa < 1:915590/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:68767/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:56799/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:149057/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa < 1:370791/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa < 1:3315497/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa < 1:2159162/69‑1 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:1524802/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:250957/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:233762/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:2319590/1‑69 (MQ=255)
gctgcGGTGAGACGCCGCCCTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGa > 1:2005020/1‑69 (MQ=255)
|
CTTACCCTAACCGAGCCTGCGCAAAAGCAATCGCCTGCGCCACCTGCTGCGGTGAGACGCCGCCTTTTGCCGCACGCTTGTCGAGGCACGATTGCAGCGACAGAATCGGATAGA > minE/2284163‑2284276
|
| 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
