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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 45.4
/ NA
| 15 | R238P (CGC→CCC) | lplA | lipoate‑‑protein ligase LplA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (6/9); total (6/9) |
GTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTC > NZ_CP009273/4613136‑4613295
|
gTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTgggggg > 1:109644/1‑90 (MQ=255)
aCGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAg > 1:99331/1‑90 (MQ=255)
aCGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAg > 2:103398/1‑90 (MQ=255)
aCGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAg > 2:349486/1‑90 (MQ=255)
ccAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGc < 2:40570/90‑1 (MQ=255)
gTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCa < 1:14153/90‑1 (MQ=255)
tCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAg > 2:127093/1‑90 (MQ=255)
ccAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTg < 1:195293/90‑1 (MQ=255)
gATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGttt < 1:121821/90‑1 (MQ=255)
aTGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCgggg < 1:41236/90‑1 (MQ=255)
tGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGga > 2:283337/1‑90 (MQ=255)
ccGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGgaga < 2:109644/90‑1 (MQ=255)
aGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCa > 1:221664/1‑90 (MQ=255)
cATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACgcgc < 1:129852/90‑1 (MQ=255)
aTTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCt < 2:486427/90‑1 (MQ=255)
ttCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTc < 1:20620/90‑1 (MQ=255)
|
GTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTC > NZ_CP009273/4613136‑4613295
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GTCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAA > NZ_CP009273/4613125‑4613312
|
GTCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGG < SRR3722092.41173/100‑1 (MQ=60)
TCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGG > SRR3722092.111507/1‑100 (MQ=60)
ATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAG > SRR3722092.101032/1‑100 (MQ=60)
ctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGG < SRR3722092.512634/53‑1 (MQ=60)
GTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGT < SRR3722092.14394/100‑1 (MQ=60)
CCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTT < SRR3722092.198529/100‑1 (MQ=60)
GATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGA < SRR3722092.123887/100‑1 (MQ=60)
ATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTC < SRR3722092.41943/100‑1 (MQ=60)
GCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCA > SRR3722092.225289/1‑100 (MQ=60)
CATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAAT < SRR3722092.132042/100‑1 (MQ=60)
TTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGG < SRR3722092.20975/100‑1 (MQ=60)
CTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATctgtctctt > SRR3722092.284915/1‑91 (MQ=60)
|
GTCGAAATGCAGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAATGGGCGAAAA > NZ_CP009273/4613125‑4613312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
