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 F5 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,032,221 |
T→C |
F6S (TTC→TCC) |
hyaF → |
hydrogenase expression/formation protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,032,221 | 0 | T | C | 100.0%
| 40.6
/ NA
| 13 | F6S (TTC→TCC) | hyaF | hydrogenase expression/formation protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/6); total (7/6) |
CGGAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTTCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCC > NZ_CP009273/1032109‑1032321
|
cggAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATctgct > 1:748992/1‑122 (MQ=255)
cggAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATctgct < 2:748992/122‑1 (MQ=255)
aCCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCTACCGAACGATGACAGTTTCAGCATGAATCCAc < 1:675991/137‑1 (MQ=255)
aCCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCAc > 2:675991/1‑137 (MQ=255)
aaCTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCAt > 1:522512/1‑117 (MQ=255)
aaCTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCAt < 2:522512/117‑1 (MQ=255)
gATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAatgat > 2:871/1‑138 (MQ=255)
tGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGt > 1:443665/1‑124 (MQ=255)
tGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGt < 2:443665/124‑1 (MQ=255)
tGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGaa > 1:523316/1‑139 (MQ=255)
aaCCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGcc < 2:307112/139‑1 (MQ=255)
ccGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATctgct < 1:323524/46‑1 (MQ=255)
ccGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATctgct > 2:323524/1‑46 (MQ=255)
|
CGGAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTTCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCC > NZ_CP009273/1032109‑1032321
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CACTTTAGTGTTTACCGGCGGAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTTCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGA > NZ_CP009273/1032091‑1032368
|
attttgcttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAA < SRR3722133.327995/69‑1 (MQ=60)
GTGTTTACCGGCGGAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACtgtctc > SRR3722133.758705/1‑145 (MQ=60)
TCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCTACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACC < SRR3722133.684770/150‑1 (MQ=60)
CCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCtgtctcttat > SRR3722133.529535/1‑140 (MQ=60)
GATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGActgtc > SRR3722133.449710/1‑146 (MQ=60)
GATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAAC > SRR3722133.530354/1‑151 (MQ=60)
ACTTTTTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTA > SRR3722133.459044/1‑150 (MQ=60)
TTCCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGA < SRR3722133.881/150‑1 (MQ=60)
|
CACTTTAGTGTTTACCGGCGGAAACTATCGCGGCGTGCTGAATGGTATTCACCCGTGGGCGGAACTGATAAACCTGATGCGCGGGCTTGTCGAACCGCAGCAGGAGCGTGCCTCATGAGCGAAACTTTTTTCCATCTGCTGGGGCCAGGAACGCAACCGAACGATGACAGTTTCAGCATGAATCCACTGCCGATCACCTGTCAGGTGAATGATGAACCGAGTATGGCGGCCCTGGAGCAATGTGCTCACAGCCCGCAGGTGATTGCGCTGTTAAACGA > NZ_CP009273/1032091‑1032368
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
