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Oryza barthii vs Leersia perrieri LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) 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

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
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 barthiiLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 246,872 alignment blocks

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

Uncovered: 171,683,408 out of 308,272,304
Covered: 136,588,896 out of 308,272,304

Uncovered: 2,917,830 out of 39,538,509
Matches: 31,115,310 out of 39,538,509
Mismatches: 4,708,614 out of 39,538,509
Insertions: 796,755 out of 39,538,509
Identity over aligned base-pairs: 85.0%

Leersia perrieri

Uncovered: 152,442,150 out of 266,687,832
Covered: 114,245,682 out of 266,687,832

Uncovered: 5,702,267 out of 36,898,596
Matches: 27,022,093 out of 36,898,596
Mismatches: 3,575,132 out of 36,898,596
Insertions: 599,104 out of 36,898,596
Identity over aligned base-pairs: 86.6%

Block size distribution

Size range All 246,872 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,703
23.5 kb
10 bp - 100 bp
43,195
2.6 Mb
18,515
1.3 Mb
100 bp - 1 kb
158,323
59.1 Mb
54,732
16.7 Mb
1 kb - 10 kb
41,637
84.1 Mb
7,242
17.2 Mb
10 kb - 100 kb
14
163.2 kb
199
4.6 Mb
100 kb - 1 Mb
14
2.2 Mb
1 Mb - 10 Mb
9
60.9 Mb
10 Mb - 100 Mb
3
43.1 Mb