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 |
579,943 |
(T)8→7 |
intergenic (+57/+193) |
appY → / ← ompT |
DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 579,936 | 0 | T | . | 100.0%
| 28.3
/ NA
| 8 | intergenic (+50/+200) | appY/ompT | DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (4/4); total (4/4) |
GATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACT > NZ_CP009273/579860‑580005
|
gATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGa < 2:359521/90‑1 (MQ=255)
aacaaTTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCAt > 1:125447/1‑90 (MQ=255)
aTTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAAt > 2:489414/1‑90 (MQ=255)
aaGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGcc < 2:125447/90‑1 (MQ=255)
aaGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGcc < 2:140217/90‑1 (MQ=255)
tGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTatacat < 1:490528/90‑1 (MQ=255)
tGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTatacat > 2:490528/1‑90 (MQ=255)
tAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACt > 2:200073/1‑90 (MQ=255)
|
GATGGAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACT > NZ_CP009273/579860‑580005
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATG > NZ_CP009273/579864‑580025
|
GAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCAT > SRR3722111.127023/1‑100 (MQ=60)
TGTTAATTATAATATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTG < SRR3722111.498067/100‑1 (MQ=60)
ATTATACAGCG‑TTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATG > SRR3722111.518832/1‑100 (MQ=60)
|
GAATAAACAAAACAATTGACTGATAATGTTTATTACAAGTTGTCTACATGTTAATTATAATATTATACAGCGTTTTTTTTGATGTGATATTCTGGAACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATG > NZ_CP009273/579864‑580025
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
