Arabidopsis thaliana vs Sorghum bicolor LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 114,198

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

Uncovered: 93,481,930 out of 119,667,750
Covered: 26,185,820 out of 119,667,750

Uncovered: 14,289,918 out of 33,774,176
Matches: 12,650,111 out of 33,774,176
Mismatches: 6,447,917 out of 33,774,176
Insertions: 386,230 out of 33,774,176

Sorghum bicolor

Uncovered: 697,903,827 out of 726,795,624
Covered: 28,891,797 out of 726,795,624

Uncovered: 18,235,899 out of 38,980,957
Matches: 13,322,145 out of 38,980,957
Mismatches: 6,917,319 out of 38,980,957
Insertions: 505,594 out of 38,980,957

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
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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Sorghum bicolor
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}