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 |
|
A1 F2 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,849,315 |
A→C |
Y540S (TAC→TCC) |
flhA → |
formate hydrogenlyase transcriptional activator FlhA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,849,315 | 0 | A | C | 100.0%
| 14.7
/ NA
| 6 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (4/2); total (4/2) |
ACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT > NZ_CP009273/2849257‑2849399
|
ccTACCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccg < 1:177801/89‑1 (MQ=255)
aaaaGGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCg < 1:124616/90‑1 (MQ=255)
gTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgctgc > 2:278514/1‑90 (MQ=255)
ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa > 1:213158/1‑90 (MQ=255)
ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa > 2:74205/1‑90 (MQ=255)
ctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCtt > 1:294779/1‑90 (MQ=255)
|
ACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT > NZ_CP009273/2849257‑2849399
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849257‑2849407
|
cctacCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCG < SRR3722116.179967/95‑1 (MQ=60)
AAAAGGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTC < SRR3722116.126105/100‑1 (MQ=60)
ACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAA > SRR3722116.215898/1‑100 (MQ=60)
GTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT > SRR3722116.299096/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722116.345965/1‑100 (MQ=60)
|
ACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849257‑2849407
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
