About CNV association

[Jingjiao-ma]

hi

I run plink v1.07 Association mapping with segmental CNV data: regional tests
the EMP1 and EMP2 of every region is 1

my vcf is

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CP1600001	CP1600002	CP1600003	CP1600004	CP1600005	CP1600006	CP1600007	CP1600008	CP1600009	CP1600010	CP1600011	CP1600012	CP1600013	CP1600014	CP1600015	CP1600016	CP1600017	CP1600018	CP1600019	CP1600020	CP1600021	CP1600022	CP1600023	CP1600024	CP1600025	CP1600026	CP1600027	CP1600028	CP1600029	CP1600030	CP1600031	CP1600032	CP1600033	CP1600034	CP1600035	CP1600036	CP1600037	CP1600038	CP1600039	CP1600040	CP1600041
1	790997	CNV_1_790997_830957	T	<CN0>,<CN2>	.	PASS	END=830957;GCFRACTION=0.43;GCLENGTH=39961;GLALTFREQ=NA;GLALTSUM=0.000;GLHETSUM=0.000;GLINBREEDINGCOEFF=NA;GLREFFREQ=NA;GLREFSUM=0.000;GSCALLRATE=0.999;GSCLUSTERSEP=9.59;GSCLUSTERSEPWEIGHTEDMEAN=8.03;GSCLUSTERSEPWEIGHTEDMEDIAN=8.14;GSCNALLELES=3;GSCNCATEGORY=MIXED;GSCNDIST=0,3,794,152,18;GSCNMAX=4;GSCNMIN=1;GSCNQUAL=2181.9075;GSDUPLICATEOVERLAP=NA;GSDUPLICATES=NA;GSDUPLICATESCORE=NA;GSELENGTH=26499;GSEXPMEAN=189.3918;GSGMMWEIGHTS=0.0001,0.0031,0.8205,0.1577,0.0186,0.0000;GSM1=1.0647;GSM2=0.3106,1.5530;GSNNONREF=173;GSNONVARSCORE=NA;GSNVARIANT=173;SVTYPE=CNV	GT:CN:CNF:CNL:CNP:CNQ:GL:GP:GQ	0/2:3:2.9985:-1000.00,-110.41,-13.72,-0.00,-7.01,-22.31:-1000.00,-112.12,-13.01,-0.00,-7.94,-59.86:79.4:-14.20,-110.41,-1000.00,-0.00,-13.90,-7.01:-12.47,-113.83,-1000.00,-0.00,-15.91,-8.95:79	0/0:2:2.2905:-1000.00,-46.59,-0.00,-3.71,-19.97,-41.26:-1000.00,-49.01,-0.00,-4.42,-21.62,-79.53:44.2:-0.48,-46.59,-1000.00,-3.71,-0.18,-19.97:-0.00,-51.26,-1000.00,-4.96,-3.44,-23.17:34	0/0:2:2.0602:-1000.00,-31.48,-0.00,-8.33,-26.61,-48.86:-1000.00,-33.90,-0.00,-9.05,-28.26,-87.12:90.5:-0.48,-31.48,-1000.00,-8.33,-0.18,-26.61:-0.00,-36.15,-1000.00,-9.59,-3.44,-29.81:34	0/0:2:2.0828:-1000.00,-34.69,-0.00,-8.34,-27.44,-50.83:-1000.00,-37.12,-0.00,-9.06,-29.08,-89.09:90.6:-0.48,-34.69,-1000.00,-8.34,-0.18,-27.44:-0.00,-39.37,-1000.00,-9.60,-3.44,-30.63:34	0/0:2:2.0486:-1000.00,-32.82,-0.00,-9.11,-28.69,-52.45:-1000.00,-35.24,-0.00,-9.82,-30.33,-90.71:98.2:-0.48,-32.82,-1000.00,-9.11,-0.18,-28.69:-0.00,-37.49,-1000.00,-10.36,-3.44,-31.88:34	0/2:3:2.9220:-1000.00,-106.42,-12.13,-0.00,-8.40,-25.00:-1000.00,-108.13,-11.42,-0.00,-9.32,-62.55:93.2:-12.61,-106.42,-1000.00,-0.00,-12.31,-8.40:-10.88,-109.84,-1000.00,-0.00,-14.32,-10.33:93	0/0:2:2.0621:-1000.00,-32.94,-0.00,-8.65,-27.68,-50.87:-1000.00,-35.36,-0.00,-9.36,-29.33,-89.13:93.6:-0.48,-32.94,-1000.00,-8.65,-0.18,-27.68:-0.00,-37.61,-1000.00,-9.90,-3.44,-30.88:34	0/0:2:1.9514:-1000.00,-25.78,-0.00,-10.57,-30.21,-53.49:-1000.00,-28.20,-0.00,-11.28,-31.86,-91.75:99.0:-0.48,-25.78,-1000.00,-10.57,-0.18,-30.21:-0.00,-30.45,-1000.00,-11.82,-3.44,-33.41:34	0/0:2:2.1869:-1000.00,-36.41,-0.00,-5.42,-21.29,-41.33:-1000.00,-38.83,-0.00,-6.14,-22.93,-79.59:61.4:-0.48,-36.41,-1000.00,-5.42,-0.18,-21.29:-0.00,-41.08,-1000.00,-6.68,-3.44,-24.48:34	0/0:2:2.0285:-1000.00,-30.43,-0.00,-9.17,-28.24,-51.25:-1000.00,-32.85,-0.00,-9.89,-29.88,-89.51:98.9:-0.48,-30.43,-1000.00,-9.17,-0.18,-28.24:-0.00,-35.10,-1000.00,-10.43,-3.44,-31.43:34	0/2:3:2.7910:-1000.00,-88.50,-8.20,-0.00,-9.81,-26.83:-1000.00,-90.21,-7.48,-0.00,-10.74,-64.37:74.8:-8.68,-88.50,-1000.00,-0.00,-8.38,-9.81:-6.94,-91.92,-1000.00,-0.00,-10.38,-11.75:69	0/0:2:1.9336:-1000.00,-24.42,-0.00,-10.74,-30.25,-53.28:-1000.00,-26.84,-0.00,-11.45,-31.90,-91.54:99.0:-0.48,-24.42,-1000.00,-10.74,-0.18,-30.25:-0.00,-29.09,-1000.00,-11.99,-3.44,-33.45:34	0/0:2:1.7895:-1000.00,-18.80,-0.00,-14.79,-37.97,-64.50:-1000.00,-21.23,-0.00,-15.51,-39.62,-102.76:99.0:-0.48,-18.80,-1000.00,-14.79,-0.18,-37.97:-0.00,-23.48,-1000.00,-16.05,-3.44,-41.17:34	2/2:4:3.7541:-1000.00,-220.35,-44.25,-5.02,-0.00,-8.66:-1000.00,-221.13,-42.61,-4.09,-0.00,-45.27:40.9:-44.73,-220.35,-1000.00,-5.02,-44.43,-0.00:-41.06,-221.83,-1000.00,-3.08,-44.50,-0.00:31	0/0:2:2.0219:-1000.00,-29.98,-0.00,-9.29,-28.38,-51.39:-1000.00,-32.41,-0.00,-10.00,-30.02,-89.65:99.0:-0.48,-29.98,-1000.00,-9.29,-0.18,-28.38:-0.00,-34.66,-1000.00,-10.54,-3.44,-31.57:34	0/0:2:1.9482:-1000.00,-25.23,-0.00,-10.48,-29.87,-52.83:-1000.00,-27.65,-0.00,-11.19,-31.52,-91.09:99.0:-0.48,-25.23,-1000.00,-10.48,-0.18,-29.87:-0.00,-29.90,-1000.00,-11.73,-3.44,-33.07:34	0/0:2:2.1870:-1000.00,-38.21,-0.00,-5.68,-22.32,-43.35:-1000.00,-40.64,-0.00,-6.40,-23.97,-81.61:64.0:-0.48,-38.21,-1000.00,-5.68,-0.18,-22.32:-0.00,-42.89,-1000.00,-6.94,-3.44,-25.52:34	0/0:2:1.9498:-1000.00,-26.13,-0.00,-10.77,-30.76,-54.44:-1000.00,-28.55,-0.00,-11.49,-32.41,-92.70:99.0:-0.48,-26.13,-1000.00,-10.77,-0.18,-30.76:-0.00,-30.80,-1000.00,-12.03,-3.44,-33.96:340/0:2:1.7935:-1000.00,-17.12,-0.00,-13.26,-34.10,-57.97:-1000.00,-19.54,-0.00,-13.97,-35.74,-96.23:99.0:-0.48,-17.12,-1000.00,-13.26,-0.18,-34.10:-0.00,-21.79,-1000.00,-14.51,-3.44,-37.29:34	0/0:2:2.0280:-1000.00,-30.71,-0.00,-9.28,-28.55,-51.81:-1000.00,-33.14,-0.00,-10.00,-30.19,-90.07:99.0:-0.48,-30.71,-1000.00,-9.28,-0.18,-28.55:-0.00,-35.39,-1000.00,-10.54,-3.44,-31.74:34	0/0:2:2.0524:-1000.00,-32.91,-0.00,-8.99,-28.45,-52.09:-1000.00,-35.33,-0.00,-9.71,-30.10,-90.35:97.1:-0.48,-32.91,-1000.00,-8.99,-0.18,-28.45:-0.00,-37.58,-1000.00,-10.25,-3.44,-31.65:34	0/2:3:3.0927:-1000.00,-128.70,-17.42,-0.00,-6.04,-21.46:-1000.00,-130.40,-16.70,-0.00,-6.97,-59.01:69.7:-17.90,-128.70,-1000.00,-0.00,-17.60,-6.04:-16.16,-132.11,-1000.00,-0.00,-19.60,-7.98:70	0/0:2:1.9925:-1000.00,-29.43,-0.00,-10.25,-30.41,-54.54:-1000.00,-31.86,-0.00,-10.97,-32.06,-92.80:99.0:-0.48,-29.43,-1000.00,-10.25,-0.18,-30.41:-0.00,-34.11,-1000.00,-11.51,-3.44,-33.61:34	0/0:2:2.1112:-1000.00,-35.29,-0.00,-7.50,-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1	791801	CNV_1_791801_893718	T	<CN0>,<CN2>	.	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1	833820	CNV_1_833820_910074	T	<CN0>,<CN2>	.	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1	833820	CNV_1_833820_921749	T	<CN2>	.	PASS	END=921749;GCFRACTION=0.49;GCLENGTH=87930;GLALTFREQ=NA;GLALTSUM=0.000;GLHETSUM=0.000;GLINBREEDINGCOEFF=NA;GLREFFREQ=NA;GLREFSUM=0.000;GSCALLRATE=0.997;GSCLUSTERSEP=11.84;GSCLUSTERSEPWEIGHTEDMEAN=9.88;GSCLUSTERSEPWEIGHTEDMEDIAN=10.03;GSCNALLELES=2;GSCNCATEGORY=DUP;GSCNDIST=0,0,794,154,17;GSCNMAX=4;GSCNMIN=2;GSCNQUAL=3150.7876;GSDUPLICATEOVERLAP=NA;GSDUPLICATES=NA;GSDUPLICATESCORE=NA;GSELENGTH=80424;GSEXPMEAN=575.1572;GSGMMWEIGHTS=0.0001,0.0001,0.8204,0.1615,0.0178,0.0000;GSM1=1.0294;GSM2=0.5779,2.8895;GSNNONREF=171;GSNONVARSCORE=NA;GSNVARIANT=171;SVTYPE=CNV	GT:CN:CNF:CNL:CNP:CNQ:GL:GP:GQ	0/1:3:2.8511:-1000.00,-142.63,-14.74,-0.00,-13.54,-38.39:-1000.00,-145.83,-14.03,-0.00,-14.50,-123.85:99.0:-14.74,-0.00,-13.54:-13.02,-0.00,-15.51:99	0/0:2:1.8504:-1000.00,-30.72,0.00,-18.70,-49.74,-85.72:-1000.00,-34.62,0.00,-19.40,-51.41,-171.89:99.0:0.00,-18.70,-49.74:0.00,-20.41,-53.42:99	0/0:2:1.9690:-1000.00,-40.22,-0.00,-15.31,-44.50,-79.23:-1000.00,-44.12,0.00,-16.02,-46.16,-165.39:99.0:-0.00,-15.31,-44.50:0.00,-17.03,-48.17:99	0/0:2:1.8924:-1000.00,-35.50,0.00,-18.26,-49.96,-87.02:-1000.00,-39.40,0.00,-18.97,-51.62,-173.18:99.0:0.00,-18.26,-49.96:0.00,-19.98,-53.63:99	0/0:2:1.9695:-1000.00,-42.62,0.00,-16.18,-47.05,-83.79:-1000.00,-46.52,0.00,-16.89,-48.71,-169.95:99.0:0.00,-16.18,-47.05:0.00,-17.90,-50.72:99	0/1:3:2.7690:-1000.00,-136.33,-12.11,-0.00,-15.91,-43.02:-1000.00,-139.52,-11.40,-0.00,-16.87,-128.48:99.0:-12.11,-0.00,-15.91:-10.39,-0.00,-17.88:990/0:2:1.9767:-1000.00,-42.36,-0.00,-15.63,-45.76,-81.67:-1000.00,-46.26,0.00,-16.34,-47.42,-167.83:99.0:-0.00,-15.63,-45.76:0.00,-17.35,-49.43:99	0/0:2:1.8824:-1000.00,-33.41,0.00,-17.89,-48.59,-84.41:-1000.00,-37.31,0.00,-18.59,-50.25,-170.58:99.0:0.00,-17.89,-48.59:0.00,-19.60,-52.26:99	0/0:2:1.8594:-1000.00,-28.83,0.00,-16.94,-45.32,-78.26:-1000.00,-32.73,0.00,-17.65,-46.98,-164.43:99.0:0.00,-16.94,-45.32:0.00,-18.66,-48.99:99	0/0:2:1.9908:-1000.00,-42.31,-0.00,-14.77,-43.79,-78.52:-1000.00,-46.21,-0.00,-15.47,-45.46,-164.68:99.0:-0.00,-14.77,-43.79:0.00,-16.48,-47.47:99	0/1:3:2.9940:-1000.00,-169.57,-21.01,-0.00,-10.87,-34.48:-1000.00,-172.77,-20.30,-0.00,-11.83,-119.94:99.0:-21.01,-0.00,-10.87:-19.29,-0.00,-12.84:99	0/0:2:1.9953:-1000.00,-41.86,-0.00,-14.36,-42.77,-76.79:-1000.00,-45.76,-0.00,-15.07,-44.43,-162.95:99.0:-0.00,-14.36,-42.77:0.00,-16.08,-46.44:99	0/0:2:1.9870:-1000.00,-45.70,0.00,-16.19,-47.83,-85.66:-1000.00,-49.60,0.00,-16.89,-49.50,-171.82:99.0:0.00,-16.19,-47.83:0.00,-17.90,-51.51:99	1/1:4:3.6896:-1000.00,-313.06,-60.84,-5.78,-0.00,-13.93:-1000.00,-315.30,-59.18,-4.82,-0.00,-98.43:48.2:-60.84,-5.78,-0.00:-57.17,-3.82,-0.00:38	0/0:2:2.0319:-1000.00,-45.76,-0.00,-13.54,-41.90,-76.18:-1000.00,-49.66,-0.00,-14.25,-43.56,-162.34:99.0:-0.00,-13.54,-41.90:-0.00,-15.26,-45.57:99	0/0:2:2.0333:-1000.00,-45.44,-0.00,-13.37,-41.44,-75.39:-1000.00,-49.34,-0.00,-14.08,-43.11,-161.55:99.0:-0.00,-13.37,-41.44:-0.00,-15.09,-45.12:99	0/0:2:2.1562:-1000.00,-54.98,-0.00,-9.46,-35.01,-67.00:-1000.00,-58.88,-0.00,-10.16,-36.68,-153.17:99.0:-0.00,-9.46,-35.01:-0.00,-11.17,-38.69:99	0/0:2:1.9784:-1000.00,-42.03,-0.00,-15.41,-45.16,-80.65:-1000.00,-45.93,0.00,-16.11,-46.83,-166.82:99.0:-0.00,-15.41,-45.16:0.00,-17.12,-48.84:99	0/0:2:2.0137:-1000.00,-43.86,-0.00,-13.97,-42.39,-76.59:-1000.00,-47.76,-0.00,-14.68,-44.06,-162.75:99.0:-0.00,-13.97,-42.39:-0.00,-15.69,-46.07:99	0/0:2:1.9737:-1000.00,-40.41,-0.00,-15.10,-44.07,-78.59:-1000.00,-44.31,-0.00,-15.81,-45.74,-164.75:99.0:-0.00,-15.10,-44.07:0.00,-16.82,-47.75:99	0/0:2:1.9964:-1000.00,-44.78,-0.00,-15.28,-45.57,-81.86:-1000.00,-48.68,0.00,-15.99,-47.24,-168.02:99.0:-0.00,-15.28,-45.57:0.00,-17.00,-49.25:99	0/1:3:2.8754:-1000.00,-157.36,-16.88,-0.00,-14.02,-40.39:-1000.00,-160.56,-16.17,-0.00,-14.98,-125.85:99.0:-16.88,-0.00,-14.02:-15.16,-0.00,-15.99:99	0/0:2:1.8722:-1000.00,-34.33,0.00,-19.14,-51.64,-89.48:-1000.00,-38.23,0.00,-19.85,-53.31,-175.65:99.0:0.00,-19.14,-51.64:0.00,-20.86,-55.32:99	0/0:2:1.9492:-1000.00,-38.77,-0.00,-15.95,-45.58,-80.66:-1000.00,-42.67,0.00,-16.66,-47.24,-166.83:99.0:-0.00,-15.95,-45.58:0.00,-17.67,-49.25:99	0/0:2:2.1130:-1000.00,-50.33,-0.00,-10.57,-36.36,-68.23:-1000.00,-54.23,-0.00,-11.28,-38.02,-154.40:99.0:-0.00,-10.57,-36.36:-0.00,-12.29,-40.03:99	0/0:2:1.9876:-1000.00,-37.96,-0.00,-13.43,-39.71,-71.11:-1000.00,-41.86,-0.00,-14.14,-41.37,-157.28:99.0:-0.00,-13.43,-39.71:-0.00,-15.15,-43.38:99	0/0:2:1.9235:-1000.00,-36.12,0.00,-16.45,-46.02,-80.85:-1000.00,-40.02,0.00,-17.15,-47.69,-167.01:99.0:0.00,-16.45,-46.02:0.00,-18.16,-49.70:99	0/1:3:2.8684:-1000.00,-163.49,-17.35,-0.00,-14.83,-42.53:-1000.00,-166.68,-16.65,-0.00,-15.79,-127.99:99.0:-17.35,-0.00,-14.83:-15.64,-0.00,-16.80:99	0/0:2:2.0436:-1000.00,-49.86,-0.00,-14.06,-44.08,-80.48:-1000.00,-53.76,-0.00,-14.76,-45.74,-166.65:99.0:-0.00,-14.06,-44.08:-0.00,-15.77,-47.75:99	0/1:3:2.7992:-1000.00,-134.65,-12.71,-0.00,-14.58,-40.08:-1000.00,-137.84,-12.01,-0.00,-15.54,-125.54:99.0:-12.71,-0.00,-14.58:-11.00,-0.00,-16.55:99	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I convert it to

FID	IID	CHR	BP1	BP2	TYPE	SCORE	SITES
CP1600001	CP1600001	1	790997	830957	3	0	0
CP1600002	CP1600002	1	790997	830957	2	0	0

then I run

plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --cnv-make-map
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --map plink.cnv.map --fam genomestrip.fam
plink-1.07-x86_64/plink --cnv-list genomestrip.cnv --map plink.cnv.map --fam genomestrip.fam --cnv-intersect glist-hg38.dms  --cnv-test-region --mperm 10000

the result is

$head plink.cnv.regional.summary.mperm
 CHR           REGION         EMP1         EMP2
   1          DDX11L1            1            1
   1           WASH7P            1            1
   1        MIR6859-1            1            1
   1        MIR1302-2            1            1
   1          FAM138A            1            1
   1            OR4F5            1            1
   1        LOC729737            1            1
   1        MIR6859-1            1            1
   1          FAM138D            1            1

Which step did I do wrong？

Best，
Maggie