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 |
2,202,171 |
G→C |
W242C (TGG→TGC) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,171 | 0 | G | C | 100.0%
| 55.8
/ NA
| 18 | W242C (TGG→TGC) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (11/7); total (11/7) |
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCG > NZ_CP009273/2202097‑2202249
|
gTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCAtt < 2:158528/90‑1 (MQ=255)
tACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTa > 1:258399/1‑90 (MQ=255)
tACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTa > 1:303136/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 1:177037/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 1:525316/1‑90 (MQ=255)
aaaGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCtggtgg < 2:177037/90‑1 (MQ=255)
aaaGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCtggtgg < 2:44042/90‑1 (MQ=255)
gATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTg > 2:332345/1‑90 (MQ=255)
gATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGacac < 2:407330/90‑1 (MQ=255)
cGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGcgt < 2:31609/90‑1 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAtctctc > 1:7152/1‑88 (MQ=255)
ctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAg > 2:476661/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc > 1:173149/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc > 2:321678/1‑90 (MQ=255)
gATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGc > 2:522451/1‑90 (MQ=255)
aTGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGcc < 2:17135/90‑1 (MQ=255)
ggcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGa < 2:75597/90‑1 (MQ=255)
gcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCg > 1:207644/1‑90 (MQ=255)
|
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCG > NZ_CP009273/2202097‑2202249
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCG > NZ_CP009273/2202073‑2202249
|
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCC < SRR3722111.533603/100‑1 (MQ=60)
CAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTA > SRR3722111.261441/1‑100 (MQ=60)
CAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTA > SRR3722111.307064/1‑100 (MQ=60)
GGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAT > SRR3722111.179254/1‑100 (MQ=60)
GGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAT > SRR3722111.533543/1‑100 (MQ=60)
ATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCTC > SRR3722111.7244/1‑100 (MQ=60)
GATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAC > SRR3722111.175309/1‑100 (MQ=60)
GGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCG > SRR3722111.210198/1‑100 (MQ=60)
|
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCG > NZ_CP009273/2202073‑2202249
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
