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Triticum aestivum vs Sorghum bicolor LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Triticum aestivum 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

ParameterTriticum aestivumSorghum bicolor
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 771,199 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 14,201,762,821 out of 14,547,261,565
Covered: 345,498,744 out of 14,547,261,565

Uncovered: 13,814,879 out of 133,674,966
Matches: 91,421,155 out of 133,674,966
Mismatches: 25,802,638 out of 133,674,966
Insertions: 2,636,294 out of 133,674,966
Identity over aligned base-pairs: 76.3%

Sorghum bicolor

Uncovered: 626,224,163 out of 708,735,318
Covered: 82,511,155 out of 708,735,318

Uncovered: 4,403,822 out of 39,785,927
Matches: 26,852,132 out of 39,785,927
Mismatches: 7,403,068 out of 39,785,927
Insertions: 1,126,905 out of 39,785,927
Identity over aligned base-pairs: 75.9%

Block size distribution

Size range All 771,199 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,347
30.1 kb
10 bp - 100 bp
102,423
6.8 Mb
45,092
3.3 Mb
100 bp - 1 kb
559,818
211.1 Mb
260,063
93.5 Mb
1 kb - 10 kb
103,530
172.2 Mb
100,944
254.9 Mb
10 kb - 100 kb
81
879.1 kb
2,759
39.3 Mb