Vindel: a simple pipeline for checking indel redundancy

Table 3 Various statistics

Chromosome	Original number of indels	Redundancy	Insertion redundancy	Indel size	Adjacent-SNP		Adjacent-indel
		rate (%) ^a	rate (%) ^b	Shape ^c	Shape ^d	Rate ^e	Shape ^f	Rate ^g
1	485270	9.63	47.99	1.44	0.83	0.016	0.39	7.55E-04
2	503609	9.57	48.18	1.43	0.86	0.016	0.4	7.57E-04
3	431820	9.38	47.57	1.47	0.89	0.017	0.4	8.03E-04
4	417942	9.98	48.62	1.47	0.89	0.017	0.39	7.82E-04
5	374774	9.49	47.06	1.46	0.88	0.017	0.4	7.53E-04
6	388741	10.16	48.14	1.43	0.84	0.017	0.39	7.99E-04
7	349376	9.68	48.38	1.43	0.86	0.017	0.4	7.96E-04
8	307212	9.55	48.56	1.47	0.88	0.018	0.4	7.72E-04
9	250802	9.29	49.25	1.45	0.82	0.016	0.4	7.37E-04
10	292264	9.58	48.23	1.42	0.85	0.017	0.39	7.82E-04
11	280673	9.6	47.66	1.46	0.87	0.017	0.4	7.72E-04
12	298606	9.65	48.73	1.45	0.87	0.017	0.4	8.16E-04
13	223181	10.31	46.21	1.39	0.9	0.017	0.38	7.95E-04
14	195779	9.8	49.23	1.46	0.88	0.017	0.4	7.94E-04
15	182417	9.77	48.87	1.44	0.85	0.016	0.4	7.86E-04
16	180020	9.41	50.29	1.39	0.81	0.018	0.4	8.09E-04
17	185888	10.03	51.8	1.4	0.83	0.016	0.4	8.40E-04
18	169830	10.02	48.61	1.41	0.89	0.017	0.4	8.07E-04
19	148904	9.93	53.31	1.39	0.81	0.018	0.41	9.69E-04
20	139927	10.54	51.3	1.4	0.88	0.018	0.39	8.16E-04
21	96577	9.3	49.52	1.45	0.85	0.018	0.4	9.83E-04
22	90621	10.31	50.46	1.33	0.83	0.018	0.39	8.77E-04
Mean	5994233^h	9.77	49	1.43	0.86	0.017	0.4	8.09E-04
STD		0.35	1.62	0.035	2.73E-02	7.61E-04	5.54E-03	6.21E-05

^aThe total redundancy rate on individual chromosomes. ^bThe percentage of redundant insertions. ^cThe shape parameter of the Pareto distributions fitted to the indel sizes (after redundancy filtration). ^d,eThe shape and rate parameter estimates for the Gamma distributions fitted to the adjacent-SNP distances. ^f,gThe shape and rate parameter estimates for the Gamma distributions fitted to the adjacent-indel distances. ^hTotal number of indels studied.