Hybrid assembly with long and short reads improves discovery of gene family expansions

BMC Genomics

Table 4 Gene copy number predictions and validations for a CRP3710 subfamily

accession:	HM101	HM034	HM056	HM340
A. Assembly
MT4.0	2
ALLPATHS		1	3	3
PBJelly		8	5	3
Alpaca		29	26	30
B. Coverage (RPM)
Medtr1g061160 (control 1)	0.26	0.38	0.29	0.50
Medtr1g080770 (control 2)	0.29	0.59	0.51	0.57
CRP3710	7.00	5.60	9.00	14.00
estimated copy number	25.5	11.5	22.5	26.2
C. qPCR
estimated copy number	12.0	11.0	9.7	8.9

A. Annotation found between 1 and 30 copies per assembly. B. Coverages in reads per million bases for this gene and two controls, followed by the copy numbers estimated by fold increase of gene over control average, per accession. C. Copy numbers estimated from quantitative PCR per accession

ISSN: 1471-2164