Oryza sativa Japonica Group vs Triticum dicoccoides LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 782,434

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

Uncovered: 289,541,363 out of 375,049,285
Covered: 85,507,922 out of 375,049,285

Uncovered: 3,131,028 out of 34,403,043
Matches: 24,169,003 out of 34,403,043
Mismatches: 6,219,229 out of 34,403,043
Insertions: 883,783 out of 34,403,043

Triticum dicoccoides

Uncovered: 9,777,863,999 out of 10,079,039,394
Covered: 301,175,395 out of 10,079,039,394

Uncovered: 19,788,334 out of 100,651,268
Matches: 62,327,755 out of 100,651,268
Mismatches: 16,476,715 out of 100,651,268
Insertions: 2,058,464 out of 100,651,268

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 Group Triticum dicoccoides
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}