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Oryza sativa Indica Group vs Leersia perrieri LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Indica Group 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 sativa Indica GroupLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 268,559 alignment blocks

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

Uncovered: 228,514,921 out of 374,545,499
Covered: 146,030,578 out of 374,545,499

Uncovered: 3,445,035 out of 42,733,995
Matches: 33,154,682 out of 42,733,995
Mismatches: 5,176,234 out of 42,733,995
Insertions: 958,044 out of 42,733,995
Identity over aligned base-pairs: 84.4%

Leersia perrieri

Uncovered: 151,460,723 out of 266,687,832
Covered: 115,227,109 out of 266,687,832

Uncovered: 4,961,830 out of 36,899,367
Matches: 27,736,135 out of 36,899,367
Mismatches: 3,630,978 out of 36,899,367
Insertions: 570,424 out of 36,899,367
Identity over aligned base-pairs: 86.8%