Triticum dicoccoides vs Triticum turgidum LastZ Results

Back to all analyses

Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum dicoccoides was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 1,996,754

Genome coverage (bp) Coding exon coverage (bp)
Triticum dicoccoides

Uncovered: 2,243,046,094 out of 10,079,039,394
Covered: 7,835,993,300 out of 10,079,039,394

Uncovered: 13,105,125 out of 81,268,905
Matches: 66,926,635 out of 81,268,905
Mismatches: 1,110,814 out of 81,268,905
Insertions: 126,331 out of 81,268,905

Triticum turgidum subsp. durum

Uncovered: 2,415,799,529 out of 10,463,058,104
Covered: 8,047,258,575 out of 10,463,058,104

Uncovered: 16,093,563 out of 88,577,667
Matches: 71,072,689 out of 88,577,667
Mismatches: 1,278,176 out of 88,577,667
Insertions: 133,239 out of 88,577,667

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac --identity=75..100

Chunking parameters

Triticum dicoccoides Triticum turgidum
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options