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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,888,711 |
A→G |
V143A (GTC→GCC) |
ygcQ ← |
electron transfer flavoprotein subunit alpha/FixB family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,888,711 | 0 | A | G | 100.0%
| 23.4
/ NA
| 9 | V143A (GTC→GCC) | ygcQ | electron transfer flavoprotein subunit alpha/FixB family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/4); total (5/4) |
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > NZ_CP009273/2888625‑2888777
|
gCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCaa < 1:215194/90‑1 (MQ=255)
cGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTc > 1:400096/1‑90 (MQ=255)
tCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGc < 2:242180/90‑1 (MQ=255)
aGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCAt < 1:6787/90‑1 (MQ=255)
aGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCAt < 2:130822/90‑1 (MQ=255)
cgcgGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCa > 1:114070/1‑90 (MQ=255)
gATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCgctg > 1:385620/1‑90 (MQ=255)
gccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCa > 1:458856/1‑90 (MQ=255)
gccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCa > 2:817/1‑90 (MQ=255)
|
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > NZ_CP009273/2888625‑2888777
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > NZ_CP009273/2888620‑2888777
|
CACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTC > SRR3722113.404280/1‑100 (MQ=60)
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTG < SRR3722113.216889/100‑1 (MQ=60)
AGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGC < SRR3722113.6856/100‑1 (MQ=60)
GCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCA > SRR3722113.115063/1‑100 (MQ=60)
ACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTG > SRR3722113.389651/1‑100 (MQ=60)
GTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > SRR3722113.463710/1‑100 (MQ=60)
|
CACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > NZ_CP009273/2888620‑2888777
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
