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Arabidopsis thaliana vs Glycine max LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 thalianaGlycine max
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 263,764 alignment blocks

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

Uncovered: 82,627,830 out of 119,667,750
Covered: 37,039,920 out of 119,667,750

Uncovered: 8,416,254 out of 33,775,569
Matches: 16,949,212 out of 33,775,569
Mismatches: 7,779,771 out of 33,775,569
Insertions: 630,332 out of 33,775,569
Identity over aligned base-pairs: 66.8%

Glycine max

Uncovered: 898,147,705 out of 978,491,270
Covered: 80,343,565 out of 978,491,270

Uncovered: 17,405,539 out of 65,618,132
Matches: 32,445,446 out of 65,618,132
Mismatches: 14,505,912 out of 65,618,132
Insertions: 1,261,235 out of 65,618,132
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 263,764 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,436
13.4 kb
10 bp - 100 bp
40,977
2.7 Mb
10,339
739.9 kb
100 bp - 1 kb
203,934
68.3 Mb
57,718
21.7 Mb
1 kb - 10 kb
16,405
24.6 Mb
27,524
64.2 Mb
10 kb - 100 kb
12
143.5 kb
565
9.2 Mb