CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

BMC Genomics

Table 5 Summary of CLARK ’s assignment of 15,665 BACs (represented as reads) to barley chromosome arms (reads) and centromeres ( k =19)

*Targets*	*19-mers*	*Discriminative 19-mers*	*Assignments*	*Low confidence*	*High confidence*
1H	448,768,897	126,997,864	2,068	4.2%	95.8%
2HC	-	1,738,722	0	-	-
2HL	451,729,142	102,959,160	1,417	2.1%	97.9%
2HS	401,605,473	79,225,936	1,071	2.4%	97.6%
3HC	-	4,631,639	0	-	-
3HL	553,420,081	138,939,217	1,423	2.2%	97.8%
3HS	538,777,930	113,354,224	892	3.5%	96.5%
4HC	-	6,428,726	70	14.3	85.7%
4HL	494,923,209	106,930,230	1,127	2.3%	97.7%
4HS	462,144,322	85,650,765	888	3.4%	96.6%
5HC	-	1,643,194	0	-	-
5HL	558,710,983	121,491,586	1,657	2.3%	97.7%
5HS	281,062,766	57,181,745	658	2.4%	97.6%
6HC	-	1,287,133	0	-	-
6HL	311,443,157	70,856,097	1,136	2.0%	98.0%
6HS	877,169,677	255,819,549	850	2.9%	97.1%
7HC	-	1,697,991	0	-	-
7HL	366,612,780	82,987,499	1,175	2.0%	98.0%
7HS	365,475,556	83,848,867	1,233	2.8%	97.2%
Total	6,111,843,973	1,443,670,144	15,665	2.7%	97.3%

Columns: (1) barley chromosome 1H, twelve chromosome arms, and six centromeres; (2) number of distinct k-mers in each target; (3) number of discriminative k-mers present in target sequences (must occur at least twice); (4) number of assigned objects per target; (5) number of low confidence assignment per target; (6) number of high confidence assignment per target; (7) percentage of low confidence assignment (as a fraction of the total number of assigned objects per target); (8) percentage of high confidence assignment (as a fraction of the total number of assigned objects per target).

ISSN: 1471-2164