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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,002,903 |
T→C |
S261P (TCA→CCA) |
ygeY → |
YgeY family selenium metabolism‑linked hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,002,903 | 0 | T | C | 100.0%
| 82.4
/ NA
| 26 | S261P (TCA→CCA) | ygeY | YgeY family selenium metabolism‑linked hydrolase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/11); total (15/11) |
TCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTTCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGA > NZ_CP009273/3002823‑3002981
|
tCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGAcc > 1:178113/1‑90 (MQ=255)
cGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACcg > 1:530775/1‑90 (MQ=255)
aaGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCgtcgtc > 1:366795/1‑90 (MQ=255)
cccTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCt > 1:125491/1‑90 (MQ=255)
ccGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCg > 2:574557/1‑90 (MQ=255)
cGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGa < 1:128509/90‑1 (MQ=255)
ttCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACcg < 2:92658/69‑1 (MQ=255)
ttCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACcg > 1:92658/1‑69 (MQ=255)
ttcttcACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGgc < 1:50305/90‑1 (MQ=255)
tCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGAc > 1:156100/1‑90 (MQ=255)
gTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCcgcg > 2:12630/1‑90 (MQ=255)
ttGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCgcgc > 1:542889/1‑90 (MQ=255)
gcgcTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGccc < 1:410101/90‑1 (MQ=255)
gcgcTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGccc < 2:275136/90‑1 (MQ=255)
gcTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCcctg < 2:328501/90‑1 (MQ=255)
gcTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCcctg < 1:68807/90‑1 (MQ=255)
gCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCa < 1:143041/90‑1 (MQ=255)
cAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAg < 1:393707/90‑1 (MQ=255)
aGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGt > 1:361499/1‑90 (MQ=255)
cAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACa > 1:199603/1‑90 (MQ=255)
cAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACa > 2:305234/1‑90 (MQ=255)
aGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAg < 1:51247/90‑1 (MQ=255)
gCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGGAACCTGGGAAGGCGCGCTGGACGa > 2:214633/1‑64 (MQ=255)
gCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGa < 1:214633/64‑1 (MQ=255)
gCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGa > 2:188599/1‑90 (MQ=255)
gCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGa > 1:377103/1‑90 (MQ=255)
|
TCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTTCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGA > NZ_CP009273/3002823‑3002981
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TATGACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTTCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGCTAACGCGGTTGTTT > NZ_CP009273/3002810‑3002999
|
GATGACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCC > SRR3722111.443650/1‑100 (MQ=60)
TGACGAATTCCTCGGCAAAGGCCCCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGAC < SRR3722111.436367/100‑1 (MQ=60)
TGACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCTAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGAC < SRR3722111.365208/100‑1 (MQ=60)
TGACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGAC < SRR3722111.383797/100‑1 (MQ=60)
GACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACC > SRR3722111.180345/1‑100 (MQ=60)
ACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCG > SRR3722111.539099/1‑100 (MQ=60)
TTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTC > SRR3722111.371953/1‑100 (MQ=60)
GGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCT > SRR3722111.127067/1‑100 (MQ=60)
CCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCctgtctcttat > SRR3722111.93798/1‑89 (MQ=60)
CGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAA < SRR3722111.130116/100‑1 (MQ=60)
CTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGAC > SRR3722111.158076/1‑100 (MQ=60)
TTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACG < SRR3722111.50914/100‑1 (MQ=60)
CCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGC > SRR3722111.551428/1‑100 (MQ=60)
tgtgtataagagacagGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCC < SRR3722111.217249/84‑1 (MQ=60)
GCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGT > SRR3722111.366533/1‑100 (MQ=60)
GCGCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGT < SRR3722111.416122/100‑1 (MQ=60)
GCTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTAC < SRR3722111.69621/100‑1 (MQ=60)
CTGTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACA > SRR3722111.202085/1‑100 (MQ=60)
GTAGCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGA > SRR3722111.382490/1‑100 (MQ=60)
GCAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAG < SRR3722111.144839/100‑1 (MQ=60)
CAGACAGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGC < SRR3722111.399415/100‑1 (MQ=60)
AGCTGCGCAGTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGCTAACG < SRR3722111.51867/100‑1 (MQ=60)
GTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGCTAACGCGGTTGTTT > SRR3722111.211815/1‑100 (MQ=60)
GTTCCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGCTAACGCGGTTGTTT > SRR3722111.437129/1‑100 (MQ=60)
|
TATGACGAATTCCTCGGCAAAGGCACCCTCACCGTTTCTGAAATCTTCTTCACATCCCCAAGCCGTTGCGCTGTAGCAGACAGCTGCGCAGTTTCAATCGACCGTCGTCTGACCTGGGGCGAAACCTGGGAAGGCGCGCTGGACGAAATCCGCGCCCTGCCTGCAGTACAGAAAGCTAACGCGGTTGTTT > NZ_CP009273/3002810‑3002999
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
