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Oryza longistaminata vs Oryza barthii LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza barthii (Oryza barthii, O.barthii_v1) 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 barthii
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 262,904 alignment blocks

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

Uncovered: 91,346,331 out of 326,442,508
Covered: 235,096,177 out of 326,442,508

Uncovered: 1,035,592 out of 34,512,301
Matches: 32,160,760 out of 34,512,301
Mismatches: 1,133,896 out of 34,512,301
Insertions: 182,053 out of 34,512,301
Identity over aligned base-pairs: 96.1%

Oryza barthii

Uncovered: 101,962,614 out of 308,272,304
Covered: 206,309,690 out of 308,272,304

Uncovered: 5,928,060 out of 39,538,509
Matches: 32,377,201 out of 39,538,509
Mismatches: 995,413 out of 39,538,509
Insertions: 237,835 out of 39,538,509
Identity over aligned base-pairs: 96.3%

Block size distribution

Size range All 262,904 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,617
22.3 kb
10 bp - 100 bp
43,511
2.6 Mb
18,750
1.2 Mb
100 bp - 1 kb
151,587
60.4 Mb
50,782
19.8 Mb
1 kb - 10 kb
63,151
163.5 Mb
12,795
31.1 Mb
10 kb - 100 kb
1,038
13.4 Mb
2,993
107.1 Mb
100 kb - 1 Mb
475
80.7 Mb