Table 2.

Read processing summary

Sample Name*	Initial reads	Filtered reads	Forward denoised reads	Reverse denoised reads	Merged reads	Non-chimeric reads
D1 surface	33,726	14,952	14,752	14,917	931	797
D2 surface	17,595	16,723	16,526	16,551	799	723
D3 surface	33,384	32,146	31,755	31,637	1817	1271
D4 surface	48,328	45,818	45,501	45,593	1821	1629
H1 surface	35,032	33,574	33,273	33,170	2402	1809
H2 surface	46,959	24,152	23,455	23,929	852	675
H3 surface	35,605	33,855	33,658	33,530	4404	2571
H4 surface	47,456	45,630	45,424	45,132	7623	3265
fSW1	31,305	12,132	11,862	12,077	901	756
fSW2	37,718	16,042	15,462	15,957	789	689
D1LS	35,469	33,859	33,731	33,722	2345	2092
D2aLS	42,909	41,188	40,991	40,858	2218	1929
D2bLS	45,379	43,625	43,536	43,418	2208	1935
D3LS	49,980	21,694	21,395	21,632	1070	896
D4LS	37,435	35,707	35,542	35,585	432	376
sSW	48,680	20,150	19,895	19,810	727	473
D1LBW1	1184	1128	1010	756	2	2
D1LBW2	45,357	44,356	44,215	44,152	5074	3846
D1BW1	36,896	35,314	35,256	35,155	2668	2095
D1BW2	40,374	38,793	38,738	38,593	4921	3011
D1CF	2251	850	838	846	28	26
D2aLBW1	41,654	20,656	20,556	20,426	300	268
D2aLBW2	41,248	39,378	39,335	39,142	1272	975
D2bLBW1	56,938	28,786	28,624	28,455	1678	1412
D2bLBW2	44,766	20,958	20,746	20,801	1358	1115
D2BW1	44,633	42,758	42,713	42,560	4011	1995
D2BW1	47,160	45,031	44,962	44,843	3203	1810
D2CF	45,370	42,968	42,906	42,772	1569	1122
D3LBW1	56,282	54,004	53,949	53,760	978	843
D3BW1	39,944	18,742	18,226	18,700	2827	1299
D3BW2	2704	2630	2604	2585	4	2
D3CF	58,380	56,053	55,982	55,422	20,583	2755
H1BW1	48,161	17,693	17,023	17,685	1803	1773
H1BW2	62,699	60,458	60,385	59,924	26,964	13,253
H1CF	63,084	60,727	60,492	60,422	9486	8717
H2BW1	53,428	22,004	21,742	21,963	1565	1253
H2BW2	48,533	22,693	22,316	22,630	1448	1108
H2CF	40,126	17,722	17,439	17,582	373	279
H3BW1	54,753	52,648	52,511	52,475	5782	4393
H3BW2	75,964	37,381	36,890	37,242	3972	3140
foSW	50,319	14,087	14,038	14,084	445	258
Total	1,810,880	1,347,029	1,337,510	1,337,723	137,291	81,536

*See Table 1 for sample name definitions