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 |
3,304,813 |
(C)7→8 |
coding (1005/1245 nt) |
mtr ← |
tryptophan transporter of high affinity |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,304,806 | 1 | . | C | 92.3%
| 38.8
/ ‑2.2
| 13 | coding (1012/1245 nt) | mtr | tryptophan transporter of high affinity |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (8/4); total (9/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.30e-01 |
GGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAGCCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACG > NC_000913/3304689‑3304928
|
ggCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCAGAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCgggg < 1:571095/139‑1 (MQ=255)
gCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTc > 1:421372/1‑139 (MQ=255)
aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGcc > 2:200132/1‑139 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCg > 1:7138/1‑139 (MQ=255)
ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCg > 2:449307/1‑139 (MQ=255)
aTGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAg < 1:328627/138‑1 (MQ=255)
aTGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAg > 2:328627/1‑138 (MQ=255)
gCTAAACCCGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACACCAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGa < 2:374926/139‑1 (MQ=255)
gCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGa < 2:7138/139‑1 (MQ=255)
ggCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGt > 1:16616/1‑139 (MQ=255)
aGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCCCCACTGGCCGGGCAAAGGGCAGCCATGCCGGTTTCAAGCCGCCCCAAACCCGAG‑CGGCGAAACCAAACCAGACTTCCAAGTTAG‑CAAACAAAccccaccgttagccga > 2:637648/1‑126 (MQ=255)
tCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCTATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaa > 2:123370/1‑139 (MQ=255)
cGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAACCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacg > 1:447075/1‑139 (MQ=255)
|
GGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAG‑CGGCCCACAGCCGAGTCGTCGAAACCAAA‑CAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACG > NC_000913/3304689‑3304928
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
