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 I1 R1
|
81 |
28.9 |
1316934 |
95.8% |
1261622 |
113.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,304,862 |
G→A |
A319V (GCT→GTT) |
mtr ← |
tryptophan transporter of high affinity |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,304,862 | 0 | G | A | 95.7%
| 70.0
/ ‑6.0
| 23 | A319V (GCT→GTT) | mtr | tryptophan transporter of high affinity |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (14/8); minor base C (1/0); total (15/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
CCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAGCCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCAGACTACGGCTGTTCA > NC_000913/3304728‑3304988
|
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCg > 2:449307/1‑139 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCg > 1:7138/1‑139 (MQ=255)
aTGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAg < 1:328627/138‑1 (MQ=255)
aTGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAg > 2:328627/1‑138 (MQ=255)
gCTAAACCCGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACACCAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGa < 2:374926/139‑1 (MQ=255)
gCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGa < 2:7138/139‑1 (MQ=255)
ggCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGt > 1:16616/1‑139 (MQ=255)
aGGAATCCGTTCGGGAACAACAG‑CCCCCCCCCCACTGGCCGGGCAAAGGGCAGCCATGCCGGTTTCAAGCCGCCCCAAACCCGAG‑CGGCGAAACCAAACCAGACTTCCAAGTTAG‑CAAACAAAccccaccgttagccga > 2:637648/1‑126 (MQ=255)
tCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCTATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaa > 2:123370/1‑139 (MQ=255)
cGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacg > 1:447075/1‑139 (MQ=255)
cagccccccccACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGc < 2:421372/135‑1 (MQ=255)
cgccccccccACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCa < 1:637648/136‑1 (MQ=255)
cccACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTg > 2:257962/1‑139 (MQ=255)
aCTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAaca > 2:513546/1‑139 (MQ=255)
gCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACg > 2:361783/1‑137 (MQ=255)
gCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACg < 1:361783/137‑1 (MQ=255)
gCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGAc > 2:550014/1‑139 (MQ=255)
gCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCg > 2:363769/1‑115 (MQ=255)
gCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCg < 1:363769/115‑1 (MQ=255)
cAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACcagcag < 1:329114/139‑1 (MQ=255)
aGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGGCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCa > 1:433047/1‑139 (MQ=255)
ccGTTTTCAAG‑CGGCTCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGTACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCAGACTACg > 1:439253/1‑139 (MQ=255)
ccGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCAGACTACg > 2:39722/1‑139 (MQ=255)
aaG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCAGACTACGGCTGTTCa > 1:112617/1‑139 (MQ=255)
|
CCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAGCCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAACTCGCTACCGCAAAGTTTGAGAACACGACCAGCAGCAGATCCAGACTACGGCTGTTCA > NC_000913/3304728‑3304988
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
