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Oryza barthii vs Oryza rufipogon LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) 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 barthiiOryza rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 145,773 alignment blocks

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

Uncovered: 38,913,956 out of 308,272,304
Covered: 269,358,348 out of 308,272,304

Uncovered: 249,741 out of 39,538,509
Matches: 38,450,475 out of 39,538,509
Mismatches: 698,405 out of 39,538,509
Insertions: 139,888 out of 39,538,509
Identity over aligned base-pairs: 97.9%

Oryza rufipogon

Uncovered: 85,216,399 out of 338,040,714
Covered: 252,824,315 out of 338,040,714

Uncovered: 4,114,363 out of 42,763,723
Matches: 37,860,915 out of 42,763,723
Mismatches: 618,689 out of 42,763,723
Insertions: 169,756 out of 42,763,723
Identity over aligned base-pairs: 98.0%

Block size distribution

Size range All 145,773 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,789
10.8 kb
10 bp - 100 bp
24,030
1.4 Mb
10,542
652.2 kb
100 bp - 1 kb
68,896
26.3 Mb
23,202
8.2 Mb
1 kb - 10 kb
45,310
155.7 Mb
6,320
15.1 Mb
10 kb - 100 kb
5,748
88.7 Mb
272
5.2 Mb
100 kb - 1 Mb
10
1.6 Mb
10 Mb - 100 Mb
12
241.3 Mb