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Oryza barthii vs Oryza glaberrima LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. 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)
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 barthiiOryza glaberrima
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 112,665 alignment blocks

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

Uncovered: 38,866,780 out of 308,272,304
Covered: 269,405,524 out of 308,272,304

Uncovered: 1,435,726 out of 39,538,509
Matches: 36,835,198 out of 39,538,509
Mismatches: 1,151,474 out of 39,538,509
Insertions: 116,111 out of 39,538,509
Identity over aligned base-pairs: 96.7%

Oryza glaberrima

Uncovered: 39,786,195 out of 316,419,574
Covered: 276,633,379 out of 316,419,574

Uncovered: 918,375 out of 36,293,721
Matches: 34,413,269 out of 36,293,721
Mismatches: 837,140 out of 36,293,721
Insertions: 124,937 out of 36,293,721
Identity over aligned base-pairs: 97.3%

Block size distribution

Size range All 112,665 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,074
6.5 kb
10 bp - 100 bp
17,421
1.0 Mb
7,901
514.7 kb
100 bp - 1 kb
50,913
18.4 Mb
27,512
10.2 Mb
1 kb - 10 kb
35,094
136.0 Mb
8,261
22.0 Mb
10 kb - 100 kb
8,163
140.3 Mb
742
16.3 Mb
100 kb - 1 Mb
42
8.2 Mb
1 Mb - 10 Mb
1
1.4 Mb
10 Mb - 100 Mb
12
237.2 Mb