Copy number variation detection using next generation sequencing read counts

Wang, Heng; Nettleton, Dan; Ying, Kai

doi:10.1186/1471-2105-15-109

BMC Bioinformatics

Table 7 This table lists the detected CNV segments that are longer than 2 Mb and presents greater than 2-fold normalized read count differences between B73 and Mo17

From: Copy number variation detection using next generation sequencing read counts

	Start Position	End Position	Mo17/B73^∗
chr 1	7,674,194	10,130,535	0.47
	73,051,891	76,150,311	0.49
	78,765,566	80,973,937	0.40
	106,020,503	108,085,310	0.46
	183,346,370	185,514,363	0.34
	185,561,332	187,744,738	0.34
	206,016,332	208,795,988	0.49
chr 2	14,327,370	17,154,616	0.49
	43,421,667	45,665,032	0.47
	53,360,846	57,062,635	0.48
	101,464,135	103,592,856	0.37
	173,361,552	175,485,424	0.46
	183,250,632	186,406,359	0.46
	209,163,585	211,227,635	0.48
	211,597,012	214,704,617	0.48
chr 3	3,653,572	5,790,383	0.44
	45,465,224	48,749,064	0.40
	82,020,005	84,053,318	0.48
	176,248,175	179,361,747	0.48
chr 4	645	2,454,064	0.45
	23,025,833	25,854,581	0.48
	136,792,400	140,387,061	0.36
	140,502,832	143,245,529	0.49
	146,672,844	148,733,733	0.44
	239,597,061	242,255,833	0.48
	243,186,165	245,433,834	0.49
chr 5	753,941	4,311,600	0.48
	5,201,605	7,723,585	0.48
	11,328,383	14,574,771	0.49
	16,611,265	19,032,650	0.44
	68,583,278	71,949,086	0.40
	156,325,001	158,697,338	0.47
	168,069,569	170,816,075	0.39
	176,121,726	179,598,151	0.43
	191,459,521	195,013,031	0.48
chr 6	25,898,308	28,476,332	0.33
	70,440,134	72,858,938	0.46
	76,981,074	80,570,101	0.46
	85,620,416	87,659,132	0.48
	102,350,617	104,422,628	0.49
	154,917,250	159,407,299	0.47
	162,488,577	165,722,159	0.48
chr 7	18,304,500	22,673,932	0.49
	25,498,467	30,547,169	0.47
	78,344,496	81,198,663	0.40
	110,502,115	113,262,773	0.49
	117,913,056	119,946,052	0.49
	120,044,241	122,233,553	0.49
chr 8	20,108,771	23,447,168	0.43
	160,011,805	166,514,647	0.45
	167,430,533	169,880,960	0.45
chr 9	38,523,842	40,732,642	0.41
	46,734,889	49,382,812	0.38
	61,499,201	64,577,206	0.39
	83,491,462	88,345,837	0.46
	118,555,633	121,557,270	0.49
	143,196,239	145,630,853	0.45
	145,813,631	150,079,829	0.46
chr 10	20,262,176	24,734,243	0.48
	39,046,734	41,852,436	0.46
	72,370,857	74,553,412	0.42
	111,247,775	116,238,001	0.46
	117,013,634	120,679,932	0.49
	121,011,209	124,203,304	0.49
	130,590,451	139,841,271	0.46

The last column Mo17/B73 represents the normalized ratio of read counts between Mo17 and B73 for the genomic region between the start position and the end position. The normalization factor c₀ = 0.493.

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ISSN: 1471-2105

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