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Arabidopsis thaliana vs Vigna radiata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaVigna radiata
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 158,973 alignment blocks

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

Uncovered: 83,704,662 out of 119,667,750
Covered: 35,963,088 out of 119,667,750

Uncovered: 8,795,828 out of 33,775,569
Matches: 16,619,484 out of 33,775,569
Mismatches: 7,780,175 out of 33,775,569
Insertions: 580,082 out of 33,775,569
Identity over aligned base-pairs: 66.5%

Vigna radiata

Uncovered: 417,760,353 out of 463,085,359
Covered: 45,325,006 out of 463,085,359

Uncovered: 9,487,065 out of 36,130,572
Matches: 17,790,716 out of 36,130,572
Mismatches: 8,177,036 out of 36,130,572
Insertions: 675,755 out of 36,130,572
Identity over aligned base-pairs: 66.8%

Block size distribution

Size range All 158,973 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,324
7.0 kb
10 bp - 100 bp
28,735
1.9 Mb
11,178
763.2 kb
100 bp - 1 kb
117,635
40.2 Mb
34,048
12.8 Mb
1 kb - 10 kb
11,278
17.4 Mb
18,068
41.4 Mb
10 kb - 100 kb
1
11.0 kb
302
4.5 Mb