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Oryza glaberrima vs Oryza sativa Indica Group LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 66. Oryza glaberrima was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza glaberrimaOryza sativa Indica Group
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 115,178 alignment blocks

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

Uncovered: 52,566,308 out of 285,037,524
Covered: 232,471,216 out of 285,037,524

Uncovered: 376,804 out of 36,404,702
Matches: 35,140,574 out of 36,404,702
Mismatches: 738,798 out of 36,404,702
Insertions: 148,526 out of 36,404,702
Identity over aligned base-pairs: 97.5%

Oryza sativa Indica Group

Uncovered: 155,876,839 out of 374,545,499
Covered: 218,668,660 out of 374,545,499

Uncovered: 9,113,504 out of 42,733,995
Matches: 33,049,144 out of 42,733,995
Mismatches: 468,457 out of 42,733,995
Insertions: 102,890 out of 42,733,995
Identity over aligned base-pairs: 98.3%