Triticum turgidum vs Triticum aestivum LastZ Results

Back to all analyses

Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum turgidum 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: 1,616,606

Genome coverage (bp) Coding exon coverage (bp)
Triticum turgidum subsp. durum

Uncovered: 1,755,766,743 out of 10,463,058,104
Covered: 8,707,291,361 out of 10,463,058,104

Uncovered: 20,694,181 out of 88,577,667
Matches: 66,594,061 out of 88,577,667
Mismatches: 1,173,737 out of 88,577,667
Insertions: 115,688 out of 88,577,667

Triticum aestivum

Uncovered: 5,947,469,820 out of 14,547,261,565
Covered: 8,599,791,745 out of 14,547,261,565

Uncovered: 64,059,838 out of 133,674,966
Matches: 68,139,580 out of 133,674,966
Mismatches: 1,339,353 out of 133,674,966
Insertions: 136,195 out of 133,674,966

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