Oryza meridionalis vs Oryza sativa Indica Group LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) 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 sativa Indica Group
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 304,044 alignment blocks

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

Uncovered: 110,277,054 out of 335,668,232
Covered: 225,391,178 out of 335,668,232

Uncovered: 468,151 out of 35,224,824
Matches: 33,409,976 out of 35,224,824
Mismatches: 1,084,701 out of 35,224,824
Insertions: 261,996 out of 35,224,824
Identity over aligned base-pairs: 96.1%

Oryza sativa Indica Group

Uncovered: 233,504,177 out of 427,004,890
Covered: 193,500,713 out of 427,004,890

Uncovered: 12,187,280 out of 45,465,969
Matches: 32,266,070 out of 45,465,969
Mismatches: 808,833 out of 45,465,969
Insertions: 203,786 out of 45,465,969
Identity over aligned base-pairs: 97.0%