Table 2.

Sequence return and mapping outcomes for PAT samples.

Sample	Method	Raw tag#	mapped to chromosomes	Percent mapped to chromosomes (P)	mapped to 3'UTRs	Percent mapped to 3'UTRs (Q)	Percent difference (P–Q)	mapped to rRNA	Percent mapped to rRNA
LAa	A	5903191	1426870	24.2	1241190	21.0	3.2	55811	0.9
LAb	A	2240223	500853	22.4	40708	1.8	20.6	441263	19.7
LAc	A	4369955	2035046	46.6	1940928	44.4	2.2	40040	0.9
LB1a	B1	3625226	1687692	46.6	1448073	39.9	6.7	100783	2.8
LB1b	B1	2465522	524793	21.3	425417	17.3	4.0	7198	0.3
LB1c	B1	4696988	1964073	41.8	931280	19.8	22.0	618325	13.2
LB1d	B1	1253316	408552	32.6	324224	25.9	6.7	5557	0.4
LB1e	B1	4690393	1550875	33.1	732746	15.6	17.5	450788	9.6
LB1f	B1	4850319	1895655	39.1	811363	16.7	22.4	631594	13.0
LB2a	B2	4087200	2166330	53.0	1876339	45.9	7.1	29626	0.7
LB2b	B2	5403906	2939240	54.4	2588520	47.9	6.5	34489	0.6
SAa	A	2732659	771700	28.2	427450	15.6	12.6	213493	7.8
SBb	A	7278302	3288851	45.2	2822544	38.8	6.4	100341	1.4
SB1a	B1	712815	432544	60.7	376695	52.8	7.9	3589	0.5
SB1b	B1	2714976	1189015	43.8	995858	36.7	7.1	17144	0.6
SB2a	B2	3843750	2456458	63.9	222117	5.8	58.1	1816784	47.3
SB2b	B2	1868146	1101186	58.9	404871	21.7	37.2	450486	24.1
SB2c	B2	965054	666876	69.1	352258	36.5	32.6	179290	18.6
imB1a	B1	1069393	377199	35.3	281192	26.3	7.0	8646	0.8
imB1b	B1	1814431	629821	34.7	523215	28.8	5.9	12947	0.7
imB1c	B1	2003382	632961	31.6	495661	24.7	6.9	20252	1.0

Sample key: LA(a,b,c) – leaf PATs, prepared using Method A; LB1(a–f) – leaf PATs, prepared using Method B1; LB2(a,b) – leaf PATs prepared using Method B2; SA(a,b) – wild-type dry seed PATs, prepared using Method A; SB1(a,b) – wild type dry seed PATs, prepared using Method B1; SB2(a,b,c) – tt2-5 dry seed PATs, prepared using Method B2; imB1(a,b,c) – wild type seed imbibed for 48 hrs, prepared using Method B1