Oryza sativa Japonica Group vs Nymphaea colorata LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Nymphaea colorata (Nymphaea colorata, ASM883128v1) 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: 141,653

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

Uncovered: 343,888,592 out of 375,049,285
Covered: 31,160,693 out of 375,049,285

Uncovered: 14,324,784 out of 34,424,450
Matches: 13,183,121 out of 34,424,450
Mismatches: 6,393,148 out of 34,424,450
Insertions: 523,397 out of 34,424,450

Nymphaea colorata

Uncovered: 377,541,697 out of 408,396,728
Covered: 30,855,031 out of 408,396,728

Uncovered: 14,408,233 out of 32,910,518
Matches: 12,074,594 out of 32,910,518
Mismatches: 5,944,226 out of 32,910,518
Insertions: 483,465 out of 32,910,518

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 Nymphaea colorata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options