Oryza meridionalis vs Leersia perrieri LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) 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 meridionalisLeersia perrieri
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 213,828 alignment blocks

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

Uncovered: 213,698,932 out of 335,668,232
Covered: 121,969,300 out of 335,668,232

Uncovered: 2,736,087 out of 35,224,824
Matches: 27,542,048 out of 35,224,824
Mismatches: 4,139,599 out of 35,224,824
Insertions: 807,090 out of 35,224,824
Identity over aligned base-pairs: 84.8%

Leersia perrieri

Uncovered: 163,437,447 out of 266,687,832
Covered: 103,250,385 out of 266,687,832

Uncovered: 7,871,825 out of 36,898,596
Matches: 25,215,356 out of 36,898,596
Mismatches: 3,289,173 out of 36,898,596
Insertions: 522,242 out of 36,898,596
Identity over aligned base-pairs: 86.9%