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 |
2,186,816 |
G→A |
79.1% |
S347S (AGC→AGT) |
nanT ← |
sialic acid transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,186,816 | 0 | G | A | 79.1%
| 78.4
/ 13.4
| 57 | S347S (AGC→AGT) | nanT | sialic acid transporter |
| Reads supporting (aligned to +/- strand): ref base G (7/5); new base A (17/28); total (24/33) |
| Fisher's exact test for biased strand distribution p-value = 3.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01 |
AGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCTACGCAGCATCC > minE/2186758‑2186878
|
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAActt > 1:1256513/1‑67 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1045086/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:992741/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:902626/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:709439/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:621380/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:550750/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:493444/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:347682/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:3049993/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:2870875/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:2846532/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1986068/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1829771/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1323857/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1071840/1‑69 (MQ=255)
aGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGt > 1:1269545/1‑69 (MQ=255)
gACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTa < 1:1262840/69‑1 (MQ=255)
cGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCcca > 1:3289922/1‑68 (MQ=255)
cGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCcca > 1:1059088/1‑68 (MQ=255)
tACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTc > 1:1677379/1‑69 (MQ=255)
tACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTc > 1:3249927/1‑69 (MQ=255)
tACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTc > 1:2645347/1‑69 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:3082167/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:110480/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:114335/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:1642629/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:56678/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:3102286/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:3210774/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:3369381/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:2702303/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:2336786/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:2075534/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:1540396/68‑1 (MQ=255)
ggAATAATCAGCAGCTGCGAGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:1020498/68‑1 (MQ=255)
cagcagCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGcc < 1:1301279/69‑1 (MQ=255)
cagcagCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGcc < 1:1197130/69‑1 (MQ=255)
cagcagCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGcc < 1:1851841/69‑1 (MQ=255)
cagcTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCAcc < 1:2467199/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2908360/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:746591/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:427834/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:873187/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:1051445/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2921528/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2763183/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2701990/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:269381/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2599445/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:2485808/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:1704803/69‑1 (MQ=255)
aGGCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:165956/69‑1 (MQ=255)
ggCCAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCGACgcagc < 1:3026156/68‑1 (MQ=255)
ccAGCAGACTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCAcc < 1:965645/46‑1 (MQ=255)
cagcagGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCTACGCAGCATcc > 1:2860769/1‑69 (MQ=255)
cagcagGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCTACGCAGCATc > 1:2457170/1‑68 (MQ=255)
|
AGACGTTTGCGCCGCCAATCGCAAATACCGGAATAATCAGCAGCTGCGAGGCCAGCAGGCTACAAACGTACGCTTTGCGGGTTCCCAGCCAGTCACCGAGGAAGCCACCTACGCAGCATCC > minE/2186758‑2186878
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
