Hordeum vulgare vs Triticum turgidum LastZ Results

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Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Hordeum vulgare 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: 5,640,000

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare subsp. vulgare

Uncovered: 3,980,358,769 out of 4,834,432,680
Covered: 854,073,911 out of 4,834,432,680

Uncovered: 2,472,657 out of 44,420,163
Matches: 37,702,255 out of 44,420,163
Mismatches: 3,699,824 out of 44,420,163
Insertions: 545,427 out of 44,420,163

Triticum turgidum subsp. durum

Uncovered: 7,830,443,914 out of 10,463,058,104
Covered: 2,632,614,190 out of 10,463,058,104

Uncovered: 5,840,858 out of 88,577,667
Matches: 73,429,752 out of 88,577,667
Mismatches: 8,528,858 out of 88,577,667
Insertions: 778,199 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

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