Table 3.

List of novel Y-STR sequence variants defined by MPS.

Y-STR	Y-STR definition; Novel sequence variants	Observed #		Aspects of novelty
DYS19	[TCTA]a ccta [TCTA]b [ref. 30]
	CE12_TCTA[13]a+b ccta[0]	1		SNP internal to repeat array, allele name is a + b − 1 for compatibility to CE
DYS385a,b	DYS385a [TTTC]a/DYS385b [GAAA]a [ref. 30] DYS385a,b [aagg]5-9 [GAAA]a (this study)
	CE9_AAGG[5]GAAA[10]	1		new combination of repeat units; upstream flanking region previously considered non-variable, but shows high level of variation in number of repeats; therefore here considered part of the repeat array as AAGG[5–9] [23] also found AAGG[9])
	CE13_AAGG[5]GAAA[14]	1
	CE15_AAGG[5]GAAA[16]	1
	CE15_AAGG[8]GAAA[13]	1
	CE16_AAGG[8]GAAA[14]	1
	CE17_AAGG[5]GAAA[18]	1
	CE18_AAGG[7]GAAA[17]	2
DYS389II	[TAGA]a [CAGA]b N48 [TAGA]c [CAGA]d [ref. 30]
	CE30_TAGA[11]CAGA[2]N[48]TAGA[13]CAGA[4]	1		shorter first CAGA array
	CE30_TAGA[9]CAGA[3]N[48]TAGA[12]CAGA[6]	2		new combination of repeat units
	CE31_TAGA[10]CAGA[3]N[48]TAGA[11]CAGA[1]TAGA[1]CAGA[5]	1		SNP internal to repeat array
	CE34_TAGA[10]CAGA[3]N[48]TAGA[15]CAGA[6]	1		longer second TAGA array
DYS390	[TAGA]a [CAGA]b [TAGA]c [CAGA]d [ref. 30] [TAGA]a [CAGA]b [TAGA]c [CAGA]d [taga]1-3 (this study)
	CE22_TAGA[14]a+cCAGA[0]CAGA[8]TAGA[2]	1		SNP internal to repeat array
	CE23_TAGA[5]CAGA[1]TAGA[9]CAGA[8]TAGA[2]	1		longer first TAGA array
	CE24_TAGA[4]CAGA[1]TAGA[10]CAGA[10]TAGA[1]	1		longer second CAGA/shorter third TAGA array
	CE24_TAGA[4]CAGA[1]TAGA[11]CAGA[7]TAGA[3]	1		longer third TAGA array
	CE24_TAGA[4]CAGA[1]TAGA[11]CAGA[8]TAGA[1]GAGA[1]	1		SNP internal to repeat array
	CE26_TAGA[4]CAGA[1]TAGA[12]CAGA[9]TAGA[2]	2		new combination of repeat units
DYS391	[TCTA]a [ref. 30]
	CE8_TCTA[8]_+50C>A rs112815242 @11,982,182 M8738/CTS1866	2		SNP in the flanking region
	CE9_TCTA[9]_+50C>A rs112815242 @11,982,182 M8738/CTS1866	2		SNP in the flanking region
	CE10_TCTA[10]_+50C>A rs112815242 @11,982,182 M8738/CTS1866	2		SNP in the flanking region
	CE11_TCTA[11]_+50C>A rs112815242 @11,982,182 M8738/CTS1866	2		SNP in the flanking region
	CE11_TCTG[1]TCTA[10]	1		SNP internal to repeat array
	CE12_TCTA[12]_+50C>A rs112815242 @11,982,182 M8738/CTS1866	1		SNP in the flanking region
DYS437	[TCTA]a [TCTG]b [TCTA]4 (STRBase, accessed on 03 Nov 2017)
	CE15_TCTG[1]TCTA[8]TCTG[2]TCTA[4]	1		SNP internal to repeat array
	CE16_TCTA[6]TCTG[1]TCTA[3]TCTG[2]TCTA[4]	1		SNP internal to repeat array
DYS438	[TTTTC]a [ref. 30]
	CE8_TTTTC[8]_+21T>C rs761843885 @12,825,969 Z10613	1		shorter array; SNP in the flanking region
	CE11_TTTTC[11]_+7A>C rs760613324 @12,825,955 L255/PF4706	1		SNP in the flanking region
DYS439	[GATA]a [ref. 30]
	CE11_GATA[11]_+3A>T SNP @12,403,567	1		SNP in the flanking region
DYS448	[AGAGAT]a N42 [AGAGAT]b [ref. 30]
	CE13_AGAGAT[5]N[42]AGAGAT[8]	1		shorter first AGAGAT array
	CE19_AGAGAT[13]N[42]AGAGAT[6]	1		shorter second AGAGAT array
	CE20.4_AGAGAT[3]AGAT[1]AGAGAT[9]N[42]AGAGAT[8]	1		indel in the repeat array
	CE23_AGAGAT[14]N[42]AGAGAT[9]	1		new combination of repeat units
	CE23_AGAGAT[15]N[42]AGAGAT[8]	1		longer first AGAGAT array
DYS458	[GAAA]a [ref. 28]
	CE14_GAAA[13]GGAA[1]	1		SNP internal to repeat array
	CE15_GAAA[14]GGAA[1]	1		SNP internal to repeat array
	CE16_GAAA[15]GGAA[1]	1		SNP internal to repeat array
	CE17_GAAA[17]_+32T>C rs549572931 @7,999,934 M11097	1		SNP in the flanking region
	CE17.2_GAAA[15]AA[1]GAAA[2]	1		indel in the repeat array
	CE19_GAAA[19]_+32T>C rs549572931 @7,999,934 M11097	1		SNP in the flanking region
	CE19_GAAG[1]GAAA[18]	1		SNP internal to repeat array
	CE19.2_GAAA[17]AA[1]GAAA[2]	1		indel in the repeat array
	CE20_GAAA[19]GGAA[1]	1		SNP internal to repeat array
DYS481	[CTT]a [ref. 30] [ctg]0-2 [CTT]a (this study)
	CE26_CTG[0]CTT[27]	1		new combination of repeat units
	CE27_CTG[0]CTT[28]	2		new combination of repeat units
	CE28_CTG[1]CTT[3]CCT[1]CTT[24]	1		SNP internal to repeat array
DYS533	[TATC]a [ref. 30]
	CE14.1_TATC[11]_−48.1->CTCTTCTAACTAT indel @16,281,301	1		indel in the flanking region
	CE15_TATC[15]	1		longer repeat unit in array
DYS570	[TTTC]a [ref. 30]
	CE16_TTTC[16]_+4T>G rs763920632 @6,993,261 PH250	1		SNP in the flanking region
	CE17_TTCC[1]TTTC[16]	1		SNP internal to repeat array
	CE17_TTTC[15]CTTC[1]TTTC[1]	1		SNP internal to repeat array
	CE19_TTTC[5]TCTC[1]TTTC[13]	1		SNP internal to repeat array
DYS576	[AAAG]a [ref. 30]
	CE17.1_AAAG[18]_+3AAA>− indel @7,185,388	1		indel in the flanking region
DYS635	[TAGA]a [TACA]b [TAGA]c [TACA]d [TAGA]e [TACA]f [TAGA]g [ref. 30]
	CE18_TAGA[8]TACA[2]TAGA[2]TACA[2]TAGA[4]	3		new combination of repeat units
	CE20_TAGA[8]CAGA[1]TAGA[1]TACA[2]TAGA[2]TACA[2]TAGA[4]	1		SNP internal to repeat array
	CE21_TAGA[9]CAGA[1]TAGA[1]TACA[2]TAGA[2]TACA[2]TAGA[4]	1		SNP internal to repeat array
	CE25_TAGA[14]TACA[3]TAGA[2]TACA[2]TAGA[4]	1		SNP internal to repeat array
DYS643	[CTTTT]a [ref. 30]
	CE11_CTTTT[11]_−7A>G SNP @15,314,125	1		SNP in the flanking region
	CE15_CTTTT[15]	1		longer repeat unit in array
Y-GATA-H4	[TCTA]a [ref. 30]
	CE13_TCTA[13]_+36A>G SNP @16,631,756 Y15322/Z34275	1		SNP in the flanking region

Abbreviations: Y-STR, Y-chromosomal short tandem repeat; MPS, massively parallel sequencing; SNP, single nucleotide polymorphism; CE, capillary electrophoresis.

For DYS19, DYS385a,b, DYS390 and DYS481, uncounted repeat units are denoted with lower-case letters within the Y-STR definition. GRCh38 chrY genomic positions are noted after the ‘@’ signs. rs# or names of SNPs/indels are provided where available.

These sequence variants, in phase with their flanking sequences, to the best of our knowledge, have not been described in the literature previously [16,17,[19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29]], strbase.nist.gov, accessed 02-Nov-2017. Comparison is detailed in Table S5.