Hi,
I used soapdenovo2 assemble one plant genome, but there are many N in the scaffolds and the N50 only 15000bp. Below is some results. I don't know why? Hope somebody can help me. Thank you very much!
Size_includeN 1339592585
Size_withoutN 305042437
Scaffold_Num 975033
Mean_Size 1373
Median_Size 120
Longest_Seq 221407
Shortest_Seq 100
Singleton_Num 803540
Average_length_of_break(N)_in_scaffold 1061
Known_genome_size NaN
Total_scaffold_length_as_percentage_of_known_genome_size NaN
scaffolds>100 842372 86.39%
scaffolds>500 119625 12.27%
scaffolds>1K 93419 9.58%
scaffolds>10K 35907 3.68%
scaffolds>100K 187 0.02%
scaffolds>1M 0 0.00%
Nucleotide_A 85568194 6.39%
Nucleotide_C 68439481 5.11%
Nucleotide_G 67296842 5.02%
Nucleotide_T 83737920 6.25%
GapContent_N 1034550148 77.23%
Non_ACGTN 0 0.00%
GC_Content 44.50% (G+C)/(A+C+G+T)
N10 59139 1741
N20 43739 4409
N30 34619 7868
N40 27474 12218
N50 21467 17745
N60 15647 25064
N70 10191 35422
N80 7208 51584
N90 931 95139
Regards,
huily
I used soapdenovo2 assemble one plant genome, but there are many N in the scaffolds and the N50 only 15000bp. Below is some results. I don't know why? Hope somebody can help me. Thank you very much!
Size_includeN 1339592585
Size_withoutN 305042437
Scaffold_Num 975033
Mean_Size 1373
Median_Size 120
Longest_Seq 221407
Shortest_Seq 100
Singleton_Num 803540
Average_length_of_break(N)_in_scaffold 1061
Known_genome_size NaN
Total_scaffold_length_as_percentage_of_known_genome_size NaN
scaffolds>100 842372 86.39%
scaffolds>500 119625 12.27%
scaffolds>1K 93419 9.58%
scaffolds>10K 35907 3.68%
scaffolds>100K 187 0.02%
scaffolds>1M 0 0.00%
Nucleotide_A 85568194 6.39%
Nucleotide_C 68439481 5.11%
Nucleotide_G 67296842 5.02%
Nucleotide_T 83737920 6.25%
GapContent_N 1034550148 77.23%
Non_ACGTN 0 0.00%
GC_Content 44.50% (G+C)/(A+C+G+T)
N10 59139 1741
N20 43739 4409
N30 34619 7868
N40 27474 12218
N50 21467 17745
N60 15647 25064
N70 10191 35422
N80 7208 51584
N90 931 95139
Regards,
huily
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