Table 1. Results of 1 bp insertion spike-in study on phix174 sequence reads.

A subset of sequence reads representing approximately 76,000 sequence reads were obtained from one lane of sequencing of phiX174. Insertions and deletions were introduced in 100%, 50% and 25% of the Sequence reads covering discrete locations in the phiX174 genome. These indels were introduced at positions 100 bp apart starting at position 100 and ending at position 5000 of the phix174 genome. As noted from columns left to right, for insertions and deletions we report separately the length of the introduced mutation, the percentage of sequence reads with an introduced mutation, the number of tested candidates, the number of true positive (TP) indels among the tested candidates, the number of predictions made by the second step of the algorithm, the sensitivity and the specificity of the prediction.

Insertions							Deletions
mutation size	spike ratio	candidates	TP in candidates	number of predictions	sensitivity	specificity	mutation size	spike ratio	candidates	TP in candidates	number of predictions	sensitivity	specificity
1	100	100	28	28	0.56	1	1	100	100	30	33	0.6	0.9996
		200	45	45	0.9	1			200	44	47	0.88	0.9996
		400	50	51	1	1			400	50	58	1	0.999
	50	100	18	17	0.32	1		50	100	17	19	0.3	0.9994
		200	36	35	0.68	1			200	36	40	0.72	0.9994
		400	46	48	0.92	1			400	48	54	0.96	0.999
	25	100	7	5	0.08	1		25	100	7	8	0.08	0.9992
		200	21	19	0.36	1			200	19	18	0.28	0.9992
		400	36	33	0.64	1			400	41	41	0.72	0.999
2	100	100	25	27	0.5	1	2	100	100	25	29	0.48	1
		200	43	48	0.86	1			200	42	52	0.84	1
		400	50	69	1	1			400	49	83	0.98	0.9996
	50	100	18	17	0.32	1		50	100	15	22	0.28	0.9996
		200	31	34	0.6	1			200	31	44	0.62	0.9994
		400	46	52	0.92	1			400	45	65	0.88	0.9994
	25	100	5	3	0.04	1		25	100	5	9	0.04	0.9994
		200	19	15	0.28	1			200	18	22	0.28	0.9994
		400	31	33	0.58	1			400	29	37	0.54	0.9992
3	100	100	29	30	0.56	1	3	100	100	28	29	0.54	1
		200	41	49	0.8	1			200	43	54	0.86	1
		400	50	75	1	1			400	49	81	0.98	0.9996
	50	100	21	21	0.36	1		50	100	19	20	0.32	0.9996
		200	34	37	0.62	1			200	34	43	0.66	0.9996
		400	43	55	0.8	1			400	47	69	0.92	0.9994
	25	100	8	7	0.1	1		25	100	7	9	0.08	0.9994
		200	19	19	0.3	1			200	21	22	0.32	0.9994
		400	34	39	0.64	0.9998			400	34	45	0.66	0.9994