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 |
323,413 |
G→A |
100% |
E180E (GAG→GAA) |
recR → |
gap repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 323,413 | 0 | G | A | 80.6%
| 64.4
/ 8.7
| 46 | E180E (GAG→GAA) | recR | gap repair protein |
| Reads supporting (aligned to +/- strand): ref base G (0/9); new base A (5/32); total (5/41) |
| Fisher's exact test for biased strand distribution p-value = 5.66e-01 |
| 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. |
AGCTTTGCGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTA > minE/323349‑323478
|
aGCTTTGTGCGCAATATTACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:2179910/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:942790/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:361657/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:3406413/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:559851/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:2772653/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:1798384/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:3213493/69‑1 (MQ=255)
aGCTTTGTGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:1164763/69‑1 (MQ=255)
tgcgcAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTgg < 1:298722/61‑1 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2777188/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2815439/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:3259937/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:3340692/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2613871/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:3327785/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:256539/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2546555/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:247021/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:3434965/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:353743/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2323801/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:230188/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2230557/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:2216114/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:79421/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:1678427/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:903662/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:1452570/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:1415768/69‑2 (MQ=255)
cAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:1289995/69‑2 (MQ=255)
ccagccGAATCGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGTcac < 1:3412976/69‑1 (MQ=255)
agccGAATCGCTCATGGCGTACCGGTTGGCGGCGAACTGGAAATGGTCGat < 1:1095693/51‑2 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:3411321/56‑1 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:2672865/56‑1 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:1896171/56‑1 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:744840/56‑1 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:1894710/56‑1 (MQ=255)
cGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:1528087/56‑1 (MQ=255)
ggCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGt < 1:2754006/49‑1 (MQ=255)
tCCGGTTGGCGGCGAGCTGGAAATGGGCGACGGCACCACGTTGTCACACTCCCTTGCCGGGCGTCATaa < 1:719439/69‑1 (MQ=255)
cgAACTGGAAATGGTCGATGGCACCACGCTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTa > 1:2764316/1‑69 (MQ=255)
cgAACTGGAAATGGTCGATGGCACCACGCTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTa > 1:242358/1‑69 (MQ=255)
cgAACTGGAAATGGTCGATGGCACCACGCTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTa > 1:2395826/1‑69 (MQ=255)
cgAACTGGAAATGGTCGATGGCACCACGCTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTa > 1:1093683/1‑69 (MQ=255)
cgAACTGGAAATGGTCGATGGCACCACGCTATCACACTCCCTTGCCGGGCGTCATAAGATTCGttttt > 1:231831/1‑68 (MQ=255)
|
AGCTTTGCGCGCAATATGACGTGGAAGCCAGCCGAATCGCTCATGGCGTTCCGGTTGGCGGCGAGCTGGAAATGGTCGACGGCACCACGTTGTCACACTCCCTTGCCGGGCGTCATAAGATTCGTTTTTA > minE/323349‑323478
|
| 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
