Oryza sativa Japonica vs Triticum urartu LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum urartu (Triticum urartu, ASM34745v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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: 143,410

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 304,512,397 out of 374,424,240
Covered: 69,911,843 out of 374,424,240

Uncovered: 6,129,279 out of 34,124,807
Matches: 21,500,232 out of 34,124,807
Mismatches: 5,740,876 out of 34,124,807
Insertions: 754,420 out of 34,124,807

Triticum urartu

Uncovered: 3,693,701,355 out of 3,747,163,292
Covered: 53,461,937 out of 3,747,163,292

Uncovered: 15,341,134 out of 36,143,424
Matches: 16,518,982 out of 36,143,424
Mismatches: 3,891,307 out of 36,143,424
Insertions: 392,001 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

Chunking parameters

Oryza sativa Japonica Triticum urartu
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}