Table 2.

Reads remaining after each bioinformatic filtering step: raw read pairs in each library; R1 and R2 after trimming by quality score (Phred ≥ 20) and length (150 bp); paired reads after performing BLAST searches where each read (R1 and R2) match a reference sequence (>95% identity and >150 bp length); paired reads where both R1 and R2 match the same reference sequence; paired reads assigned to each fragment (18S, FC, Leray, Folmer) based on the read position alignment (Figure 2) on the reference sequence, as reported in the BLAST results

Library	Raw read pairs	Trimmed‐R1	Trimmed‐R2	BLAST matches	BLAST matches identical	18S	FC	Leray	Folmer
1a	786,961	732,060	613,404	324,738	207,556	39,923	4,062	151,626	11,945
1b	854,975	815,425	773,465	472,101	407,426	92,011	55,333	238,036	22,046
1c	929,743	902,841	875,974	584,322	503,691	166,998	73,084	231,414	32,195
1d	884,801	853,816	820,011	338,938	215,921	123,502	15,556	71,483	5,380
1e	914,893	887,362	861,284	533,725	443,829	153,957	61,232	187,120	41,520
1 g	781,706	751,895	725,703	462,968	380,403	103,268	49,898	212,793	14,444
2a	925,818	896,816	879,586	679,961	637,883	216,345	81,245	306,006	34,287
2b	1,036,566	1,009,121	963,326	504,939	454,293	163,410	91,998	177,804	21,081
2c	1,619,499	1,529,135	1,444,012	549,010	321,592	97,184	123,404	14,002	87,002
2d	760,043	738,317	718,755	574,756	383,888	76,266	55,724	220,464	31,434
2e	915,977	890,991	872,002	665,676	550,787	161,688	67,174	272,534	49,391
2 g	933,645	891,848	862,069	464,301	405,228	84,980	58,609	242,543	19,096
3a1	864,551	808,857	758,339	460,992	451,683	106,024	16,847	309,430	19,382
3a2	620,639	599,186	562,566	344,398	343,891	165,357	14,056	154,023	10,455
3a3	848,115	807,089	749,840	487,477	486,745	207,189	23,719	237,827	18,010
3b1	665,830	646,399	618,519	391,294	370,523	49,843	87,122	228,910	4,648
3b2	598,325	582,154	560,215	360,447	344,473	45,137	80,649	216,754	1,933
3b3	604,169	551,276	516,445	254,613	245,801	39,495	7,421	198,880	5
3c1	878,572	837,934	796,782	639,100	453,527	71,604	37,155	325,269	19,499
3c2	984,226	945,575	896,894	734,085	514,066	87,262	56,390	336,935	33,479
3c3	947,283	906,549	856,936	708,977	509,943	75,427	61,220	348,371	24,925
3d1	845,249	734,376	670,594	494,308	409,633	52	104,521	295,096	9,964
3d2	826,818	773,111	732,549	594,312	486,103	266	167,564	301,917	16,356
3d3	702,450	615,365	563,521	418,385	323,118	33	139,858	164,883	18,344
Average	863,786	821,146	778,866	501,826	410,500	96,968	63,910	226,838	22,784
STD	200,992	194,408	189,389	129,699	104,787	62,575	41,850	81,269	18,427