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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 21.9
/ NA
| 8 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (4/4); total (4/4) |
ACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGAT > NZ_CP009273/2849237‑2849370
|
acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg > 2:131905/1‑90 (MQ=255)
cgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGt < 2:44995/90‑1 (MQ=255)
cGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCACGCCTGAACGTATTc < 2:114652/90‑1 (MQ=255)
ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc > 1:358961/1‑90 (MQ=255)
aCTACCCCCGATCTAAAAAAAAGGGTCCCCGCCCGGGAGTCCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTgccg < 1:124429/90‑1 (MQ=255)
aaCCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCa > 1:422695/1‑90 (MQ=255)
aaaaTGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCg < 2:392510/90‑1 (MQ=255)
gTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat > 1:489014/1‑90 (MQ=255)
|
ACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGAT > NZ_CP009273/2849237‑2849370
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849227‑2849407
|
ATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACG < SRR3722094.97606/100‑1 (MQ=60)
CGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACC > SRR3722094.364972/1‑100 (MQ=60)
CGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCA > SRR3722094.430073/1‑100 (MQ=60)
ACTACCCCCGATCTAAAAAAAAGGGTCCCCGCCCGGGAGTCCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCG < SRR3722094.126215/100‑1 (MQ=46)
GAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGAT > SRR3722094.497631/1‑100 (MQ=60)
TCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATT > SRR3722094.165656/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722094.510036/1‑100 (MQ=60)
|
ATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > NZ_CP009273/2849227‑2849407
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
