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Zea mays vs Sorghum bicolor LastZ results

Zea mays (Zea mays, Zm-B73-REFERENCE-NAM-5.0) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. Zea mays 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

ParameterZea maysSorghum bicolor
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 587,461 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 1,983,599,343 out of 2,182,075,994
Covered: 198,476,651 out of 2,182,075,994

Uncovered: 2,406,982 out of 43,681,835
Matches: 37,280,361 out of 43,681,835
Mismatches: 3,458,584 out of 43,681,835
Insertions: 535,908 out of 43,681,835
Identity over aligned base-pairs: 90.3%

Sorghum bicolor

Uncovered: 578,258,220 out of 708,735,318
Covered: 130,477,098 out of 708,735,318

Uncovered: 4,271,280 out of 39,785,927
Matches: 31,054,433 out of 39,785,927
Mismatches: 3,711,290 out of 39,785,927
Insertions: 748,924 out of 39,785,927
Identity over aligned base-pairs: 87.4%

Block size distribution

Size range All 587,461 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,424
33.5 kb
10 bp - 100 bp
124,417
7.8 Mb
51,567
3.6 Mb
100 bp - 1 kb
400,076
131.6 Mb
213,133
68.7 Mb
1 kb - 10 kb
57,504
108.9 Mb
25,679
53.8 Mb
10 kb - 100 kb
40
472.8 kb
898
22.4 Mb
100 kb - 1 Mb
74
23.7 Mb
1 Mb - 10 Mb
25
76.7 Mb