Oryza sativa Japonica Group vs Gossypium raimondii LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Gossypium raimondii (Gossypium raimondii, Graimondii2_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: 178,696

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

Uncovered: 339,723,991 out of 375,049,285
Covered: 35,325,294 out of 375,049,285

Uncovered: 13,775,608 out of 34,403,043
Matches: 13,249,000 out of 34,403,043
Mismatches: 6,869,391 out of 34,403,043
Insertions: 509,044 out of 34,403,043

Gossypium raimondii

Uncovered: 716,468,882 out of 761,405,269
Covered: 44,936,387 out of 761,405,269

Uncovered: 15,490,129 out of 45,523,048
Matches: 19,621,030 out of 45,523,048
Mismatches: 9,772,309 out of 45,523,048
Insertions: 639,580 out of 45,523,048

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 Gossypium raimondii
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}