Table 1. Chao1 and Shannon indices of Chd1 mutant and wild-type sample replicates.

Three sets of filtering parameters were used to analyse the data.

		filtering parameters 11			filtering param. 22		filtering param. 33
		mean number of sequences	Chao1 species richness estimate	Shannon diversity index	Chao1	Shannon	Chao1	Shannon
	R1	217,999	250.43	3.37	927.71	3.75	227.43	3.38
	R2	200,030	269.5	2.91	939.22	3.27	274.0	2.92
Chd1WT/WT	R3	243,807	267.33	4.33	828.6	4.63	247.20	4.34
	mean	220,612	262.42	3.54	898.51	3.88	249.54	3.55
	R1	232,649	206.25	2.04	636.64	2.12	196.25	2.01
	R2	342,146	195.07	1.3	367.67	1.34	173.13	1.30
Chd1-/-	R3	214,971	214.12	1.45	664.44	1.44	197.55	1.38
	mean	263,255	205.15	1.60	556.25	1.63	188.97	1.57
P-value	<0.05		0.00225**	0.02535*	0.05475	0.01312*	0.02667*	0.02379*

¹ discard OTUs with <0.005% of total # of reads and OTUs with reads in <2 replicates.

² discard OTUs with <10 reads and OTUs with higher # of reads in blank compared to sample [10].

³ discard OTUs with <0.005% of total # of reads and OTUs with reads in <2 replicates and OTUs with higher # of reads in blank.

* P-value < 0.05

** P-value < 0.01