Table 1.

Sequencing Statistics.

Batch a	T1a	T2a	T3a	M1a	M2a	Na
At Known Sites
Total bases mapped	120.8	135.6	130.1	137.2	123.3	119.1
Mean depth	42.3	47.5	45.5	48.0	43.1	41.7
Coverage (%)	97.93	97.93	97.9	97.91	97.89	97.96
No. of SNPs Detected (Q ≥ 20)
SNPs	3,690,282	3,680,844	3,678,250	3,679,869	3,648,729	3,691,527
Transition/transversion	2.06	2.06	2.06	2.06	2.06	2.06
Heterogeneous/homogeneous	1.5	1.48	1.48	1.48	1.46	1.49
Concordance with Quad SNPs (%)	99.89	99.85	99.83	99.74	99.63	99.89
In dbSNP (%)	93.8	93.7	93.8	94	93.9	93.9
No. of Indels Detected (Q ≥ 20, length ≤ 300)
Insertions	311,033	309,245	305,466	318,674	293,919	315,539
Deletions	329,908	329,198	327,838	338,497	316,097	331,755
Breakpoints	26,636	26,536	25,823	28,802	24,867	27,365

Batch b	T1b	T2b	T3b	M1b	M2b	Nb
At Known Sites
Total bases mapped	110.3	112.5	100.7	102.3	106.3	99.8
Mean depth	38.6	39.3	35.2	35.8	37.2	34.9
Coverage (%)	97.9	97.95	97.84	97.92	97.92	97.85
No. of SNPs Detected (Q ≥ 20)
SNPs	3,655,604	3,659,173	3,658,838	3,616,641	3,621,011	3,661,077
Transition/transversion	2.06	2.05	2.06	2.06	2.06	2.06
Heterogeneous/homogeneous	1.48	1.47	1.48	1.46	1.45	1.48
Concordance with Quad SNPs (%)	99.28	99.27	99.28	99.27	99.25	99.26
In dbSNP (%)	93.8	93.7	93.8	94	93.9	93.9
No. of Indels Detected (Q ≥ 20, length ≤ 300)
Insertions	295,118	306,338	293,880	280,595	285,086	295,240
Deletions	313,896	321,806	311,007	301,312	304,709	312,708
Breakpoints	9,605	9,860	9,073	8,447	9,062	9,224