Hordeum vulgare vs Triticum urartu LastZ Results

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Hordeum vulgare (Hordeum vulgare, ASM32608v1) and Triticum urartu (Triticum urartu, ASM34745v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 287,740

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

Uncovered: 4,497,262,189 out of 4,706,173,842
Covered: 208,911,653 out of 4,706,173,842

Uncovered: 6,033,621 out of 27,615,842
Matches: 19,980,450 out of 27,615,842
Mismatches: 1,419,528 out of 27,615,842
Insertions: 182,243 out of 27,615,842

Triticum urartu

Uncovered: 3,610,510,245 out of 3,747,163,292
Covered: 136,653,047 out of 3,747,163,292

Uncovered: 12,876,185 out of 36,143,424
Matches: 21,631,646 out of 36,143,424
Mismatches: 1,463,568 out of 36,143,424
Insertions: 172,025 out of 36,143,424

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
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 --matchcount=1000

Chunking parameters

Hordeum vulgare Triticum urartu
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 801,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}