Oryza sativa Japonica Group vs Galdieria sulphuraria LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Galdieria sulphuraria (Galdieria sulphuraria, ASM34128v1) 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: 8,356

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

Uncovered: 373,320,870 out of 375,049,285
Covered: 1,728,415 out of 375,049,285

Uncovered: 33,183,717 out of 34,403,043
Matches: 766,375 out of 34,403,043
Mismatches: 425,436 out of 34,403,043
Insertions: 27,515 out of 34,403,043

Galdieria sulphuraria

Uncovered: 12,742,296 out of 13,712,004
Covered: 969,708 out of 13,712,004

Uncovered: 7,499,058 out of 8,395,974
Matches: 561,326 out of 8,395,974
Mismatches: 312,640 out of 8,395,974
Insertions: 22,950 out of 8,395,974

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 Galdieria sulphuraria
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}