Oryza sativa Japonica vs Hordeum vulgare LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Hordeum vulgare (Hordeum vulgare, Hv_IBSC_PGSB_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 310,667

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

Uncovered: 299,111,836 out of 374,424,240
Covered: 75,312,404 out of 374,424,240

Uncovered: 3,850,883 out of 34,124,807
Matches: 23,388,216 out of 34,124,807
Mismatches: 6,051,107 out of 34,124,807
Insertions: 834,601 out of 34,124,807

Hordeum vulgare

Uncovered: 4,713,893,515 out of 4,833,907,081
Covered: 120,013,566 out of 4,833,907,081

Uncovered: 6,138,522 out of 44,392,268
Matches: 29,622,451 out of 44,392,268
Mismatches: 7,639,758 out of 44,392,268
Insertions: 991,537 out of 44,392,268

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 Hordeum vulgare
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}