Oryza barthii vs Oryza rufipogon LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza barthii 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

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza barthiiOryza rufipogon
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 145,773 alignment blocks

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

Uncovered: 38,913,956 out of 308,272,304
Covered: 269,358,348 out of 308,272,304

Uncovered: 249,741 out of 39,538,509
Matches: 38,450,475 out of 39,538,509
Mismatches: 698,405 out of 39,538,509
Insertions: 139,888 out of 39,538,509
Identity over aligned base-pairs: 97.9%

Oryza rufipogon

Uncovered: 85,216,399 out of 338,040,714
Covered: 252,824,315 out of 338,040,714

Uncovered: 4,113,004 out of 42,764,129
Matches: 37,862,602 out of 42,764,129
Mismatches: 618,761 out of 42,764,129
Insertions: 169,762 out of 42,764,129
Identity over aligned base-pairs: 98.0%