Scientific Data

Table 2 Assembly quality metrics.

From: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

										Subsampled
	GA25	GA32	454	LC25	LC32	LE25	LE32	MP25	MP32	MP25	MP32
Contig metrics
No of transcripts	73,139	40,440	23,725	65,998	37,718	71,508	41,307	108,623	48,400	74,623	46,505
Read mapping metrics
% fragments mapped	92	94	82	92	95	92	95	91	86	90	93
% good mappings	82	84	71	83	84	83	84	79	74	79	80
% bases uncovered	24	0	6	25	0	23	0	15	0	15	0
Comparative metrics
% contigs with CRBB	48	51	76	51	55	46	50	27	44	39	44
% refs with CRBB	60	58	49	60	59	60	59	60	59	59	59
Reference coverage	60	59	37	60	59	60	60	61	59	60	59
TransRate score
TransRate assembly score	0.2343	0.4564	0.3438	0.2367	0.4666	0.2587	0.4607	0.2746	0.3795	0.2755	0.4183
% good contigs	66	80	81	70	77	71	81	75	76	68	75
BUSCO score
% complete	92	90	62	93	91	93	90	93	91	93	90
% duplicated	47	21	18	45	20	44	21	41	23	39	23
% fragmented	1.5	1.4	16	1.6	2.0	1.4	2.4	1.1	1.7	0.9	2.3
% missing	5.5	7.7	20	4.6	6.7	5.2	7.2	5.7	6.9	5.3	7.1

A subset of the assembly quality metrics calculated by TransRate using the trimmed read sequences and E. salsugineum protein set, on assemblies constructed at kmer values of 25 and 32. BUSCO score for estimate of assembly completeness.

Back to article page

Search

Advanced search

Quick links