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Arabidopsis thaliana vs Oryza glaberrima LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. Arabidopsis thaliana 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

ParameterArabidopsis thalianaOryza 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 108,190 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 94,473,639 out of 119,667,750
Covered: 25,194,111 out of 119,667,750

Uncovered: 15,062,750 out of 33,775,569
Matches: 12,151,698 out of 33,775,569
Mismatches: 6,193,826 out of 33,775,569
Insertions: 367,295 out of 33,775,569
Identity over aligned base-pairs: 64.9%

Oryza glaberrima

Uncovered: 288,819,933 out of 316,419,574
Covered: 27,599,641 out of 316,419,574

Uncovered: 17,600,711 out of 36,293,721
Matches: 12,064,542 out of 36,293,721
Mismatches: 6,184,519 out of 36,293,721
Insertions: 443,949 out of 36,293,721
Identity over aligned base-pairs: 64.5%

Block size distribution

Size range All 108,190 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
892
4.6 kb
10 bp - 100 bp
16,518
1.1 Mb
2,899
207.7 kb
100 bp - 1 kb
84,355
28.2 Mb
20,972
8.8 Mb
1 kb - 10 kb
6,425
9.5 Mb
14,141
29.1 Mb
10 kb - 100 kb
47
754.3 kb