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Oryza longistaminata vs Leersia perrieri LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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
Masking count (M)
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 longistaminataLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 251,603 alignment blocks

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

Uncovered: 191,910,193 out of 326,442,508
Covered: 134,532,315 out of 326,442,508

Uncovered: 2,329,499 out of 34,512,301
Matches: 27,550,385 out of 34,512,301
Mismatches: 4,082,944 out of 34,512,301
Insertions: 549,473 out of 34,512,301
Identity over aligned base-pairs: 85.6%

Leersia perrieri

Uncovered: 156,835,431 out of 266,687,832
Covered: 109,852,401 out of 266,687,832

Uncovered: 7,576,942 out of 36,898,596
Matches: 25,392,701 out of 36,898,596
Mismatches: 3,389,734 out of 36,898,596
Insertions: 539,219 out of 36,898,596
Identity over aligned base-pairs: 86.6%

Block size distribution

Size range All 251,603 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,567
22.7 kb
10 bp - 100 bp
41,778
2.6 Mb
17,730
1.2 Mb
100 bp - 1 kb
166,381
62.5 Mb
59,304
19.4 Mb
1 kb - 10 kb
39,869
78.5 Mb
9,736
25.4 Mb
10 kb - 100 kb
8
89.3 kb
2,040
67.3 Mb
100 kb - 1 Mb
190
30.3 Mb