Oryza meridionalis vs Oryza barthii LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza barthii (Oryza barthii, O.barthii_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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 meridionalisOryza barthii
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 236,783 alignment blocks

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

Uncovered: 131,332,375 out of 335,668,232
Covered: 204,335,857 out of 335,668,232

Uncovered: 881,670 out of 35,224,824
Matches: 32,649,497 out of 35,224,824
Mismatches: 1,351,383 out of 35,224,824
Insertions: 342,274 out of 35,224,824
Identity over aligned base-pairs: 95.1%

Oryza barthii

Uncovered: 124,467,361 out of 308,272,304
Covered: 183,804,943 out of 308,272,304

Uncovered: 7,268,495 out of 39,538,509
Matches: 31,244,619 out of 39,538,509
Mismatches: 823,869 out of 39,538,509
Insertions: 201,526 out of 39,538,509
Identity over aligned base-pairs: 96.8%