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 6 The m-HMM segmentation result for chromosome 6 from 35.3 Mb to 57.0 Mb

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

Start Position	End Position	Mo17 Read counts	B73 Read counts	Mo17/B73^∗
35,274,511	36,847,009	1,511	2291	1.33
36,847,028	36,986,070	81	242	0.67
36,988,155	39,227,681	2,375	3850	1.21
39,227,711	39,392,612	53	294	0.36
39,392,816	39,998,180	605	810	1.51
39,998,210	40,070,876	114	95	2.43
40,071,001	42,219,831	1,978	2751	1.45
42,221,884	42,272,394	3	305	0.01
42,273,061	42,279,935	0	37	0.00
42,281,369	42,467,432	6	484	0.02
42,467,722	42,510,527	0	199	0.00
42,520,362	42,588,228	10	134	0.15
42,589,445	42,592,668	0	16	0.00
42,600,850	42,949,605	41	734	0.11
42,957,788	43,020,977	0	213	0.00
43,021,808	43,021,808	1	0	50.00
43,021,875	43,034,674	0	20	0.00
43,050,012	43,156,464	7	214	0.06
43,159,602	43,239,996	0	110	0.00
43,240,069	43,240,069	4	1	8.11
43,240,496	43,253,531	0	25	0.00
43,270,468	43,367,135	27	396	0.13
43,382,243	43,436,720	0	211	0.00
43,437,634	43,437,634	1	0	50.00
43,437,664	43,438,342	0	19	0.00
43,440,089	43,466,314	8	146	0.11
43,466,499	43,502,281	0	183	0.00
43,502,441	43,502,441	1	0	50.00
43,504,419	43,516,326	0	3	0.00
43,532,757	43,802,344	29	815	0.077
43,802,387	43,809,486	0	214	0.00
43,809,952	43,809,952	4	0	50.00
43,809,982	43,811,684	0	47	0.00
43,812,791	43,828,685	1	128	0.01
43,833,620	43,862,804	0	121	0.00
43,863,025	43,863,025	1	0	50.00
43,866,525	43,959,900	0	164	0.00
43,959,976	43,960,274	2	10	0.40
43,960,449	43,984,663	0	95	0.00
43,991,670	44,242,537	24	498	0.09
44,247,904	44,297,744	0	50	0.00
44,297,961	44,297,961	1	0	50.00
44,299,769	44,341,066	0	252	0.00
44,341,857	46,215,928	371	2308	0.32
46,215,958	46,834,832	572	895	1.29
46,835,472	47,130,192	74	545	0.27
47,130,202	47,668,306	642	833	1.56
47,681,491	47,739,876	18	72	0.50
47,740,273	47,740,273	0	2	0.00
47,746,723	48,880,371	283	1356	0.42
48,880,568	48,923,056	0	51	0.00
48,923,160	49,722,664	213	1128	0.38
49,722,844	50,132,724	231	298	1.57
50,132,929	50,239,093	28	119	0.47
50,260,756	52,852,085	2,487	3567	1.41
52,852,089	52,958,397	155	130	2.41
52,958,403	53,950,690	918	1453	1.28
53,951,899	56,137,418	895	3196	0.56
56,142,451	56,472,218	296	570	1.05
56,472,614	56,863,324	102	570	0.36
56,866,117	57,022,366	123	212	1.17

The first two columns are the start position and the end position of each of the CNV segments. Column 3 and column 4 are the read counts for Mo17 and B73 between the start position and the end position, respectively. The last column is the normalized read count ratio between Mo17 and B73, i.e., $log (\frac{Mo17}{c_{0} \cdot B73})$ for that CNV segment.
*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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