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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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%
| 77.0
/ NA
| 25 | R238P (CGC→CCC) | lplA | lipoate‑‑protein ligase LplA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (15/10); total (15/10) |
AGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCA > NZ_CP009273/4613135‑4613299
|
aGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGgggg > 2:473144/1‑90 (MQ=255)
ccACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCaa < 1:66971/90‑1 (MQ=255)
gccCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTc > 2:234494/1‑90 (MQ=255)
gccCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTc > 1:579409/1‑90 (MQ=255)
aaGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGttt > 1:30429/1‑90 (MQ=255)
aaGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGttt > 1:417962/1‑90 (MQ=255)
gCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTgg > 2:29947/1‑90 (MQ=255)
cGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGc < 1:473144/90‑1 (MQ=255)
gTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCa < 1:523522/90‑1 (MQ=255)
tCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAg > 1:57817/1‑90 (MQ=255)
gATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGttt < 1:59756/90‑1 (MQ=255)
gATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGttt < 2:209244/90‑1 (MQ=255)
gATGCGAGAATGCAGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTCGGCAAGTCTGGCGttt < 1:442122/90‑1 (MQ=255)
aTGCGAGACTGCCGGCCCCTGCCCTCAGTTCCATTCCCAGCTTCTTTGGGGGCCAAAGGGTTCGGCGAAGGTTGGCAAGTCTGGCGattt > 1:421919/1‑90 (MQ=255)
cGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGtt < 2:579409/90‑1 (MQ=255)
tGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGga > 2:101772/1‑90 (MQ=255)
gAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAgatga < 1:29947/90‑1 (MQ=255)
gACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCg > 1:575838/1‑90 (MQ=255)
gACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCg > 2:136379/1‑90 (MQ=255)
gAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTc > 1:398333/1‑90 (MQ=255)
aGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCa > 1:101356/1‑90 (MQ=255)
ccATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCAcgcg > 1:388056/1‑90 (MQ=255)
cATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACgcgc < 1:101772/90‑1 (MQ=255)
cATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACgcgc < 1:179285/90‑1 (MQ=255)
cAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCa > 1:552911/1‑90 (MQ=255)
cAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCa > 1:189597/1‑90 (MQ=255)
|
AGTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCA > NZ_CP009273/4613135‑4613299
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ 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
GTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAAT > NZ_CP009273/4613136‑4613303
|
GTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTC > SRR3722109.588184/1‑100 (MQ=60)
CCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGC < SRR3722109.67769/100‑1 (MQ=60)
GCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTT > SRR3722109.30798/1‑100 (MQ=60)
GCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTT > SRR3722109.424082/1‑100 (MQ=60)
GGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAG > SRR3722109.58503/1‑100 (MQ=60)
CGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCG < SRR3722109.480274/100‑1 (MQ=60)
GTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGT < SRR3722109.531499/100‑1 (MQ=60)
GATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGA < SRR3722109.60472/100‑1 (MQ=60)
GATGCGAGAATGCAGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTCGGCAAGTCTGGCGTTTTGTTCGGGGA < SRR3722109.448682/100‑1 (MQ=60)
GCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCG > SRR3722109.584567/1‑100 (MQ=60)
GAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTC < SRR3722109.30314/100‑1 (MQ=60)
GAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTC > SRR3722109.404068/1‑100 (MQ=60)
GCCTGACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCA > SRR3722109.102622/1‑100 (MQ=60)
gatgtgtataagagacagCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGC < SRR3722109.88145/82‑1 (MQ=60)
GACCGAAGTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCG > SRR3722109.393607/1‑100 (MQ=60)
GTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCA > SRR3722109.561320/1‑100 (MQ=60)
GTTCCATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCA > SRR3722109.191927/1‑100 (MQ=60)
CATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAAT < SRR3722109.181489/100‑1 (MQ=60)
CATTCCCAGCTACTCTGGGGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAAT < SRR3722109.103045/100‑1 (MQ=60)
|
GTTCCACGCCGCCCCAGGTAAAGCGTTCATCCAGCAGATGCGAGAATGCCGGAGCCTGACCGAAGTTCCATTCCCAGCTACTCTGGCGGGCAAAGGTTTCGGCGAAGTTTGGCAAGTCTGGCGTTTTGTTCGGGGAGATGATTTCCGCTTCCACGCGCTCGCCATAAT > NZ_CP009273/4613136‑4613303
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
