Table 1.

Statistics of good‐quality reads mapped onto the tomato and nematode reference genomes.

Sample	Replicate 1				Replicate 2
	No. of read pairs aligned onto Solanum lycopersicum genome	Percentage read pairs aligned (%)	No. of read pairs aligned onto Meloidogyne incognita genome	Percentage read pairs aligned (%)	No. of reads aligned onto Solanum lycopersicum genome	Percentage reads aligned (%)	No. of reads aligned onto Meloidogyne incognita genome	Percentage reads aligned (%)
PR_stage_0	67 446 974	92.4	10 687	0.0	11 923 705	95.0	498	0.0
PR_UI_stage_1	66 575 269	89.4	21 248	0.0	23 296 422	93.9	1777	0.0
PR_UI_stage_2	48 847 742	91.6	107	0.0	36 674 766	95.4	1044	0.0
PR_UI_stage_3	49 304 943	82.7	1169	0.0	8 761 649	94.0	822	0.0
PR_UI_stage_4	58 326 864	78.4	1065	0.0	41 281 223	93.8	3273	0.0
PR_UI_stage_5	78 560 558	90.2	1111	0.0	39 893 121	92.7	1672	0.0
PR_I_stage_1	72 787 284	90.7	62 935	0.1	22 781 784	91.2	10 552	0.0
PR_I_stage_2	54 697 086	84.8	102 658	0.2	11 485 953	94.6	8366	0.1
PR_I_stage_3	76 668 601	90.9	663 329	0.8	29 797 293	91.0	252 817	0.8
PR_I_stage_4	52 626 967	85.8	827 860	1.4	15 107 463	90.1	358 995	2.1
PR_I_stage_5	63 581 675	74.9	5 377 656	6.3	11 078 964	81.2	1 026 425	7.5
MM_stage_0	57 113 244	92.1	114	0.0	50 439 346	93.2	2658	0.0
M36_stage_0	79 366 778	92.0	205	0.0	23 983 409	95.1	498	0.0
M36_UI_stage_1	24 077 820	88.4	19 314	0.1	36 635 563	94.0	2657	0.0
M36_UI_stage_2	20 417 489	74.6	39 740	0.1	34 522 313	95.4	779	0.0
M36_I_stage_1	82 496 591	89.9	54 895	0.1	15 613 149	94.5	12 528	0.1
M36_I_stage_2	78 517 115	90.5	89 928	0.1	32 888 657	94.7	47 024	0.1

Replicate 1, paired‐end reads; Replicate 2, single‐end reads; I, infected; UI, uninfected; PR, Pusa Ruby (susceptible cultivar); MM, Money Maker (susceptible cultivar); M36, transgenic MM (resistant line).