Oryza sativa Japonica Group vs Rosa chinensis LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) 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: 178,143

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

Uncovered: 340,842,864 out of 375,049,285
Covered: 34,206,421 out of 375,049,285

Uncovered: 13,459,335 out of 34,424,450
Matches: 13,639,399 out of 34,424,450
Mismatches: 6,786,360 out of 34,424,450
Insertions: 539,356 out of 34,424,450

Rosa chinensis

Uncovered: 474,252,490 out of 515,588,973
Covered: 41,336,483 out of 515,588,973

Uncovered: 18,337,818 out of 43,773,732
Matches: 16,506,520 out of 43,773,732
Mismatches: 8,318,927 out of 43,773,732
Insertions: 610,467 out of 43,773,732

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 Rosa chinensis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options