Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas

Table 2 Mutation profiles and indels of the four adenomas

Sample	Filtering steps	Variant calling	SNPs	Somatic mutations^a	Gold set^b	Mutations/Mbp^c	Indels^d
A1	9,717	9,021	8,586	367	359	21	80
A2	7,681	7,194	7,095	56	37	3	2
A3	10,632	8,704	7,328	168	87	10	20
A4	10,594	8,826	8,516	180	172	11	31

^aMutations retained after manual inspection.
^bMutations with frequency ≥4% and occurring in >6 different read positions.
^cMbp on target are 17.2, 16.7, 16.5, and 17.1 for A1, A2, A3, and A4, respectively.
^dOnly high frequency indels are shown (frequency ≥20%). Overall, only three indels introduced frameshifts and likely activated the non-sense mediated decay (Table S2 in Additional file 3). These modifications were not considered for clustering and tree reconstruction because their frequency cannot be precisely measured.

ISSN: 1474-760X