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Oryza longistaminata vs Oryza nivara LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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 longistaminataOryza nivara
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 256,996 alignment blocks

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

Uncovered: 89,441,394 out of 326,442,508
Covered: 237,001,114 out of 326,442,508

Uncovered: 904,271 out of 34,512,301
Matches: 32,392,519 out of 34,512,301
Mismatches: 1,048,602 out of 34,512,301
Insertions: 166,909 out of 34,512,301
Identity over aligned base-pairs: 96.4%

Oryza nivara

Uncovered: 128,808,237 out of 337,950,324
Covered: 209,142,087 out of 337,950,324

Uncovered: 7,456,510 out of 42,562,444
Matches: 33,780,590 out of 42,562,444
Mismatches: 1,050,053 out of 42,562,444
Insertions: 275,291 out of 42,562,444
Identity over aligned base-pairs: 96.2%

Block size distribution

Size range All 256,996 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,473
21.5 kb
10 bp - 100 bp
41,914
2.5 Mb
17,522
1.1 Mb
100 bp - 1 kb
147,233
59.2 Mb
47,935
19.0 Mb
1 kb - 10 kb
63,219
165.3 Mb
12,953
32.7 Mb
10 kb - 100 kb
1,157
14.8 Mb
3,521
118.1 Mb
100 kb - 1 Mb
423
70.8 Mb