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Oryza glaberrima vs Oryza brachyantha LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 67. Oryza glaberrima 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 glaberrimaOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 226,574 alignment blocks

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

Uncovered: 201,883,838 out of 316,419,574
Covered: 114,535,736 out of 316,419,574

Uncovered: 6,566,073 out of 36,293,721
Matches: 25,648,169 out of 36,293,721
Mismatches: 3,488,790 out of 36,293,721
Insertions: 590,689 out of 36,293,721
Identity over aligned base-pairs: 86.3%

Oryza brachyantha

Uncovered: 166,324,184 out of 260,838,168
Covered: 94,513,984 out of 260,838,168

Uncovered: 7,626,719 out of 33,473,466
Matches: 22,851,695 out of 33,473,466
Mismatches: 2,603,644 out of 33,473,466
Insertions: 391,408 out of 33,473,466
Identity over aligned base-pairs: 88.4%

Block size distribution

Size range All 226,574 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,272
21.1 kb
10 bp - 100 bp
38,728
2.4 Mb
15,113
1.0 Mb
100 bp - 1 kb
151,066
54.8 Mb
48,662
14.5 Mb
1 kb - 10 kb
33,498
65.0 Mb
5,691
13.1 Mb
10 kb - 100 kb
10
111.7 kb
181
4.3 Mb
100 kb - 1 Mb
3
432.7 kb
1 Mb - 10 Mb
9
51.0 Mb
10 Mb - 100 Mb
3
37.9 Mb