Oryza longistaminata vs Oryza sativa Indica Group LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza longistaminata 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: 322,566

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 75,195,824 out of 326,442,508
Covered: 251,246,684 out of 326,442,508

Uncovered: 1,165,532 out of 34,512,301
Matches: 32,095,565 out of 34,512,301
Mismatches: 1,082,217 out of 34,512,301
Insertions: 168,987 out of 34,512,301

Oryza sativa Indica Group

Uncovered: 212,523,064 out of 427,004,890
Covered: 214,481,826 out of 427,004,890

Uncovered: 11,711,034 out of 45,465,969
Matches: 32,480,592 out of 45,465,969
Mismatches: 1,030,908 out of 45,465,969
Insertions: 243,435 out of 45,465,969

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 longistaminata Oryza sativa Indica Group
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}