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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,717,969 |
T→C |
E237G (GAA→GGA) |
glyQ ← |
glycine‑‑tRNA ligase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,717,969 | 0 | T | C | 100.0%
| 123.1
/ NA
| 36 | E237G (GAA→GGA) | glyQ | glycine‑‑tRNA ligase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/12); total (24/12) |
GATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCG > NZ_CP009273/3717887‑3718046
|
gaTGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAgcgc > 2:739308/1‑90 (MQ=255)
tGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCca > 2:1055979/1‑90 (MQ=255)
ttACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCagcagc > 2:525165/1‑90 (MQ=255)
tACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAgct > 2:218206/1‑90 (MQ=255)
cgcgCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATCCGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAgctgc < 1:817979/90‑1 (MQ=255)
cATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTgcg > 2:962236/1‑90 (MQ=255)
cATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTgcg > 1:1136602/1‑90 (MQ=255)
cagcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttc < 1:814664/90‑1 (MQ=255)
cagcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttc < 1:79425/90‑1 (MQ=255)
gcagGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGcttctt > 1:304407/1‑90 (MQ=255)
gTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTtctc > 1:714724/1‑90 (MQ=255)
ttGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCg > 2:450477/1‑90 (MQ=255)
aaGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTAc < 1:1055979/90‑1 (MQ=255)
aaGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTAc < 1:957056/90‑1 (MQ=255)
tgtgGGTGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCt > 2:956803/1‑90 (MQ=255)
ggcTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCa < 2:531630/90‑1 (MQ=255)
gcTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAg > 1:1068731/1‑90 (MQ=255)
gcTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAg > 2:620998/1‑90 (MQ=255)
tCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGa < 1:1188732/90‑1 (MQ=255)
tACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGa < 1:739308/90‑1 (MQ=255)
tACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGa < 1:597721/90‑1 (MQ=255)
tACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGa < 1:173172/90‑1 (MQ=255)
tACGCTCATAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGa < 1:43358/90‑1 (MQ=255)
cGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAg > 1:1015419/1‑90 (MQ=255)
cGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAg > 1:940758/1‑90 (MQ=255)
cGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCca > 2:343046/1‑90 (MQ=255)
gTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCcac > 1:960995/1‑90 (MQ=255)
cTGGCAGCGGCAGCGGATTTCCCAGTGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcg > 2:312004/1‑90 (MQ=255)
cTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcg > 2:447147/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 2:453582/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 2:222011/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 2:729150/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 2:907199/1‑90 (MQ=255)
ggcagcggcagcGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCcgcg > 1:695744/1‑90 (MQ=255)
ggcagcggATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCg > 2:511488/1‑90 (MQ=255)
ggcagcggATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCATATTCg < 1:285385/90‑1 (MQ=255)
|
GATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCG > NZ_CP009273/3717887‑3718046
|
| 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
ACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGAAGTTGTAAG > NZ_CP009273/3717872‑3718056
|
ACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCC < SRR3722089.1230748/100‑1 (MQ=60)
GCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCG > SRR3722089.1153891/1‑100 (MQ=60)
CGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATCCGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTT < SRR3722089.829455/100‑1 (MQ=60)
CGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTT > SRR3722089.308274/1‑100 (MQ=60)
CATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTC > SRR3722089.724019/1‑100 (MQ=60)
CAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTAC < SRR3722089.826062/100‑1 (MQ=60)
CAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTAC < SRR3722089.80396/100‑1 (MQ=60)
AAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGC < SRR3722089.1071827/100‑1 (MQ=60)
AAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGC < SRR3722089.971131/100‑1 (MQ=60)
GCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAG > SRR3722089.1084772/1‑100 (MQ=60)
TTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAG > SRR3722089.1030546/1‑100 (MQ=60)
TTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAG > SRR3722089.954534/1‑100 (MQ=60)
TCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTC < SRR3722089.1206810/100‑1 (MQ=60)
GAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCAC > SRR3722089.975164/1‑100 (MQ=60)
TACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATC < SRR3722089.748986/100‑1 (MQ=60)
TACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATC < SRR3722089.605044/100‑1 (MQ=60)
TACGCTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATC < SRR3722089.175338/100‑1 (MQ=60)
TACGCTCATAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATC < SRR3722089.43901/100‑1 (MQ=60)
CTCGTAGGCTGGCAGCGGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCG > SRR3722089.704814/1‑100 (MQ=60)
GGCAGCGGATTTCCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCATATTCGAAGTTGTAAG < SRR3722089.289033/100‑1 (MQ=60)
|
ACGCTCGGTGACGGAGATGGCTTTACGCGCATCCAGCAGGTTGAAGCTGTGGGCGGCTTTCAGAATACGCTCGTAGGCTGGCAGCGGCAGCGGATTTTCCAGCGCCAGCAGCTGCTGCGCTTCTTTCTCGTACTGCTCGAAGCAGGTGAACAGGAAGTCCACATCCGCGTATTCGAAGTTGTAAG > NZ_CP009273/3717872‑3718056
|
| 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: ‑ |
