Table 2.

Summary of Nuclear and Organelle filtered reads and mapping on transcriptome.

	Nuclear raw reads						Organelle reads
	Root-B1	Root-B2	Leaf-B1	Leaf-B2	Fruit-B1	Fruit-B2	Root-B1	Root-B2	Leaf-B1	Leaf-B2	Fruit-B1	Fruit-B2
No. of filtered reads	51,182,470	50,284,040	31,073,232	26,484,038	54,568,358	47,708,844	6,498,474	5,099,940	43,284,538	34,270,502	10,196,270	4,666,456
Number of reads aligned back to the assembly	48,254,832	47,774,866	27,428,342	24,243,488	49,198,832	43,710,842	6,457,534	5,065,260	43,210,954	34,212,242	10,155,484	4,652,456
Alignment %	94.28	95.01	88.27	91.54	90.16	91.62	99.37	99.32	99.83	99.83	99.6	99.7