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Arabidopsis thaliana vs Sorghum bicolor LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 thalianaSorghum bicolor
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 113,676 alignment blocks

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

Uncovered: 93,564,931 out of 119,667,750
Covered: 26,102,819 out of 119,667,750

Uncovered: 14,344,102 out of 33,775,569
Matches: 12,583,906 out of 33,775,569
Mismatches: 6,461,225 out of 33,775,569
Insertions: 386,336 out of 33,775,569
Identity over aligned base-pairs: 64.8%

Sorghum bicolor

Uncovered: 679,971,627 out of 708,735,318
Covered: 28,763,691 out of 708,735,318

Uncovered: 19,025,642 out of 39,785,927
Matches: 13,316,654 out of 39,785,927
Mismatches: 6,935,834 out of 39,785,927
Insertions: 507,797 out of 39,785,927
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 113,676 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
813
4.4 kb
10 bp - 100 bp
17,507
1.2 Mb
3,037
218.0 kb
100 bp - 1 kb
88,843
29.3 Mb
22,515
9.5 Mb
1 kb - 10 kb
6,513
9.5 Mb
14,700
29.9 Mb
10 kb - 100 kb
33
412.6 kb