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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,613,222 |
C→G |
R238P (CGC→CCC) |
lplA ← |
lipoate‑‑protein ligase LplA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,613,222 | 0 | C | G | 100.0%
| 32.3
/ NA
| 10 | R238P (CGC→CCC) | lplA | lipoate‑‑protein ligase LplA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (7/3); total (7/3) |
AGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAA > NZ_CP009273/4613135‑4613302
|
aGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGgggg > 2:238833/1‑90 (MQ=255)
tCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCa > 1:236263/1‑90 (MQ=255)
aCGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAg > 1:354442/1‑90 (MQ=255)
tCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAg > 1:450943/1‑90 (MQ=255)
cATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACgcgc < 2:37595/90‑1 (MQ=255)
aTTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCt > 1:24061/1‑90 (MQ=255)
ttCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTc < 1:148087/90‑1 (MQ=255)
cAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCa > 2:115804/1‑90 (MQ=255)
cTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATaa > 2:255367/1‑90 (MQ=255)
aCTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGgaggt > 1:529823/1‑58 (MQ=255)
aCTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAgat < 2:529823/60‑1 (MQ=255)
|
AGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAA > NZ_CP009273/4613135‑4613302
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
GAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAG > NZ_CP009273/4613128‑4613314
|
GAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCA > SRR3721989.240502/1‑100 (MQ=60)
ATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAG > SRR3721989.361242/1‑100 (MQ=60)
GGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAG > SRR3721989.460369/1‑100 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacagACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTC < SRR3721989.447288/66‑1 (MQ=60)
CCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCT > SRR3721989.24477/1‑100 (MQ=60)
ATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGGTGATTTCCGgtctgtctcttatacacatctg > SRR3721989.541178/1‑78 (MQ=60)
TTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGG < SRR3721989.150767/100‑1 (MQ=60)
ACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAG > SRR3721989.266265/1‑100 (MQ=60)
ACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAG > SRR3721989.282643/1‑100 (MQ=60)
|
GAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAAAG > NZ_CP009273/4613128‑4613314
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
