# This table shows what percentage of genes are dark by MAPQ, stratefied by genebody element
# gene_name : Ensembl gene name
# biotype : GENCODE biotype of gene
# biotype : percent of CDS bases that are dark by MAPQ within gene (non protein-coding genes will have value of -1)
# perc_UTR : percent of UTR bases that are dark by MAPQ within gene (non protein-coding genes will have value of -1(
# perc_exon : percent of exonic bases that are dark by MAPQ
# perc_intron : percent of intronic bases that are dark by MAPQ
# perc_total : percent of total gene that is dark by MAPQ
gene_name	biotype	perc_CDS	perc_UTR	perc_exon	perc_intron	perc_total
AL627309.5	other	-1.000000	-1.000000	14.368744	7.101925	8.487711
CICP7	pseudogene	-1.000000	-1.000000	36.995153	68.807339	40.713012
AC244669.2	pseudogene	-1.000000	-1.000000	0.000000	14.616415	14.513642
AC244669.1	pseudogene	-1.000000	-1.000000	0.000000	24.234211	23.871366
AC244015.2	pseudogene	-1.000000	-1.000000	75.806452	60.289229	61.204306
AC245595.1	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
RNA5SP529	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC245595.2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
FP700111.1	lincRNA	-1.000000	-1.000000	0.000000	26.051720	25.817234
RNA5SP59	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
RNU6-1071P	snRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
NUDT4P2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AL512310.11	other	-1.000000	-1.000000	0.000000	0.424132	0.422592
POTEB2	protein coding	0.000000	0.000000	0.000000	0.218908	0.206839
LINC02203	protein coding	0.000000	6.924198	4.089539	13.033929	9.310218
OR11K1P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC135068.4	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC135068.7	lincRNA	-1.000000	-1.000000	3.703704	3.619632	3.638017
POTEB	protein coding	42.752294	74.285714	44.046921	20.058815	22.397527
AC134980.3	protein coding	6.729758	2.930403	4.490501	4.434454	4.435404
AC138969.2	pseudogene	-1.000000	-1.000000	0.040278	1.558626	0.850444
AC126755.2	protein coding	0.000000	0.000000	0.000000	0.000000	4.222170
AC126755.4	lincRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
MIR3180-3	miRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
MIR3670-3	miRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC126755.3	lincRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
MIR3179-3	miRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
NOMO2	protein coding	7.602883	32.199118	14.232337	6.431039	6.748064
ABHD17AP9	pseudogene	-1.000000	-1.000000	9.323583	1.669449	3.121819
AC138869.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TP53TG3C	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
AC141257.2	lincRNA	-1.000000	-1.000000	69.573284	4.206926	4.491934
FP325313.1	pseudogene	-1.000000	-1.000000	90.313390	99.047839	98.703098
AC233699.1	pseudogene	-1.000000	-1.000000	20.222793	60.085457	59.064630
ARL17B	protein coding	0.000000	0.000000	0.000000	0.801873	0.779194
NSFP1	pseudogene	-1.000000	-1.000000	1.088435	10.723278	10.598849
RGPD5	protein coding	82.305978	66.131335	76.770884	57.622096	60.044351
ZBTB45P1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
LINC01123	lincRNA	-1.000000	-1.000000	49.392835	100.000000	81.634901
AC108938.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
RGPD6	protein coding	56.376944	76.756757	62.604828	43.042655	45.472046
CU633967.1	lincRNA	-1.000000	-1.000000	93.706453	66.064487	70.016165
CU639417.2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
LINC01669	lincRNA	-1.000000	-1.000000	49.642857	53.395473	52.990918
RF00019	other	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CU633906.1	lincRNA	-1.000000	-1.000000	93.639208	96.252538	96.054862
CU633906.4	pseudogene	-1.000000	-1.000000	0.000000	1.578791	1.205367
CBSL	protein coding	0.000000	14.371859	5.310063	7.504158	7.254758
U2AF1L5	protein coding	0.000000	19.706960	14.392723	0.470662	2.254406
CU638689.4	lincRNA	-1.000000	-1.000000	84.100921	95.298394	93.226865
CU638689.3	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CU638689.2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CU638689.5	lincRNA	-1.000000	-1.000000	95.150339	98.221846	97.262290
FP475955.1	lincRNA	-1.000000	-1.000000	7.789855	3.712534	3.770272
CU634019.6	lincRNA	-1.000000	-1.000000	1.175154	2.195839	2.032700
CU634019.5	pseudogene	-1.000000	-1.000000	80.065005	90.652557	88.023317
CU634019.2	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
CU634019.1	lincRNA	-1.000000	-1.000000	92.901537	69.782541	71.628671
RF00019	other	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CU634019.7	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CU634019.3	other	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CU633904.3	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CU633904.1	lincRNA	-1.000000	-1.000000	100.000000	99.590844	99.627099
RF00019	other	-1.000000	-1.000000	100.000000	-1.000000	100.000000
SMIM11B	protein coding	0.000000	0.000000	0.000000	1.426056	1.255663
CR381653.1	lincRNA	-1.000000	-1.000000	0.000000	0.589963	0.564417
LINC01660	lincRNA	-1.000000	-1.000000	0.000000	1.748124	1.471894
GGT3P	pseudogene	-1.000000	-1.000000	0.000000	3.517288	3.377119
E2F6P1	pseudogene	-1.000000	-1.000000	34.811828	-1.000000	34.811828
USP17L24	protein coding	16.914830	-1.000000	16.914830	0.000000	14.556638
USP17L25	protein coding	10.184634	-1.000000	10.184634	7.777778	9.841107
KCNIP4	protein coding	0.000000	0.000000	0.000000	0.380829	0.379697
DUX4	protein coding	-1.000000	50.263312	50.263312	91.944444	9.985207
PGC	protein coding	0.000000	0.000000	0.000000	0.377801	0.333372
TNRC18P3	pseudogene	-1.000000	-1.000000	0.000000	0.171809	0.144835
SLC29A4P1	pseudogene	-1.000000	-1.000000	60.824742	43.552894	46.376086
AC105233.5	other	-1.000000	-1.000000	0.000000	0.138276	0.131053
KCNB2	protein coding	0.000000	0.000000	0.000000	0.766786	0.759930
AC090735.1	lincRNA	-1.000000	-1.000000	0.000000	47.683881	44.281354
REXO1L2P	pseudogene	-1.000000	-1.000000	100.000000	98.589342	99.322289
FGF7P3	pseudogene	-1.000000	-1.000000	0.000000	4.232560	4.207584
RF00156	snRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CR769767.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
ANKRD20A2	protein coding	26.901743	81.696854	42.989085	0.815066	4.310205
BX664727.2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
BX664727.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CNN2P2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
GXYLT1P3	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AL591471.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AMYH02020865.1	pseudogene	-1.000000	-1.000000	3.099917	2.047536	2.102163
BMS1P14	lincRNA	-1.000000	-1.000000	0.000000	1.771879	1.754213
AL590399.4	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
FKBP4P7	pseudogene	-1.000000	-1.000000	9.544787	-1.000000	9.544787
AL669942.2	pseudogene	-1.000000	-1.000000	4.166667	-1.000000	4.166667
AL669942.1	other	-1.000000	-1.000000	3.921569	4.548901	10.565514
BX005195.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
NXF2	protein coding	0.000000	0.000000	0.000000	42.774581	41.491742
FAM197Y6	pseudogene	-1.000000	-1.000000	9.302326	6.212970	7.234865
TSPY3	protein coding	65.423729	26.223776	55.849701	56.532508	56.138473
TTTY2	lincRNA	-1.000000	-1.000000	42.942848	59.124584	56.270959
TTTY1	lincRNA	-1.000000	-1.000000	28.272827	8.656510	9.501727
TUBB1P2	pseudogene	-1.000000	-1.000000	1.992337	6.734007	3.905540
FAM224B	lincRNA	-1.000000	-1.000000	100.000000	99.911700	99.918379
RNA5SP520	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
RNA5SP521	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CLUHP1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TAF9P1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC007742.2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CDY5P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC007742.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
PRYP1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ACTG1P2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
XKRY	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP23	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP27	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRAPPC2P3	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
OFD1P1Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ELOCP6	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY2B	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
CDY6P	pseudogene	-1.000000	-1.000000	94.782609	37.134503	82.473586
CDY8P	pseudogene	-1.000000	-1.000000	16.431925	25.227964	18.272219
CDY2A	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
ELOCP12	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
OFD1P2Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRAPPC2P8	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP15	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP16	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
XKRY2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ACTG1P11	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
PRYP2	pseudogene	-1.000000	-1.000000	100.000000	99.678589	99.689112
ELOCP26	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY9P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TAF9P2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CLUHP2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
FAM224A	lincRNA	-1.000000	-1.000000	100.000000	99.911714	99.918389
RNA5SP522	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
RNA5SP523	rRNA	-1.000000	-1.000000	100.000000	-1.000000	100.000000
ELOCP7	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
HSFY1	protein coding	93.110647	73.186634	83.933934	72.120141	72.867209
OFD1P5Y	pseudogene	-1.000000	-1.000000	0.000000	0.139655	0.131876
HSFY2	protein coding	93.110647	73.612228	84.067164	48.019290	64.663348
ELOCP14	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
HSFY5P	pseudogene	-1.000000	-1.000000	62.987013	27.536232	41.488020
USP9YP17	pseudogene	-1.000000	-1.000000	52.374101	79.555846	77.267289
PRY2	protein coding	40.990991	28.625473	33.063864	74.206729	72.108367
AC007359.1	lincRNA	-1.000000	-1.000000	62.389937	39.849070	41.392758
AC008175.1	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
TTTY6	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
PRY	protein coding	15.540541	28.499369	23.848019	56.560122	54.892739
CDY13P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
USP9YP24	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
HSFY7P	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
OFD1P9Y	pseudogene	-1.000000	-1.000000	29.463087	54.723612	53.580926
BPY2	protein coding	100.000000	78.629396	83.426573	76.526692	76.843835
AC006366.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TRIM60P8Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ZNF736P3Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRIM60P9Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RF00156	snRNA	-1.000000	-1.000000	10.948905	-1.000000	10.948905
REREP1Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC009947.1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RBMY2CP	pseudogene	-1.000000	-1.000000	66.176471	61.082231	61.698152
HSFY6P	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP18	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CDY14P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
ELOCP16	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
PRYP3	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
XKRYP3	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP25	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP29	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RAB9AP1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TRAPPC2P9	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
OFD1P11Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ELOCP9	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY15P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
XKRYP4	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
USP9YP13	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP11	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TTTY3B	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP12	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RAB9AP5	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRAPPC2P10	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
OFD1P12Y	pseudogene	-1.000000	-1.000000	100.000000	99.890866	99.896866
ELOCP10	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY1B	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
CDY17P	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
GOLGA6L11P	pseudogene	-1.000000	-1.000000	93.600617	81.497797	84.017758
AC023274.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CSPG4P3Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC012005.2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
GOLGA2P2Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
UBE2Q2P4Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
LINC00265-2P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CICP2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
LINC00266-2P	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC012005.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
RBMY2XP	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TTTY17B	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRIM60P5Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ZNF736P12Y	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TTTY4B	lincRNA	-1.000000	-1.000000	88.104089	24.898512	27.216685
BPY2B	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
AC010153.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TRIM60P10Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ZNF736P2Y	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
TRIM60P11Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ZNF736P1Y	pseudogene	-1.000000	-1.000000	2.588235	-1.000000	2.588235
AC006338.1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ZNF736P5Y	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
BPY2C	protein coding	100.000000	70.604148	77.202797	55.167732	56.172781
ZNF736P4Y	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
AC006386.1	pseudogene	-1.000000	-1.000000	72.463768	61.461794	67.921897
RBMY2YP	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC006386.2	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
LINC00266-4P	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
CICP1	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
UBE2Q2P5Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
GOLGA2P3Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC006328.2	pseudogene	-1.000000	-1.000000	100.000000	99.750407	99.760790
CSPG4P4Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
AC006328.1	pseudogene	-1.000000	-1.000000	7.142857	-1.000000	7.142857
CDY20P	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
CDY1	protein coding	100.000000	100.000000	100.000000	100.000000	100.000000
ELOCP34	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
OFD1P13Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRAPPC2P5	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RAB9AP2	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP30	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TTTY3	lincRNA	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP9	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP19	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
XKRYP5	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY22P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
ELOCP17	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
OFD1P18Y	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
TRAPPC2P4	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
RAB9AP3	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
USP9YP20	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
USP9YP21	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
XKRYP6	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
PRYP4	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
ELOCP11	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
CDY23P	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000
USP9YP26	pseudogene	-1.000000	-1.000000	100.000000	100.000000	100.000000
HSFY8P	pseudogene	-1.000000	-1.000000	96.214511	100.000000	98.503741
RBMY2DP	pseudogene	-1.000000	-1.000000	12.024221	2.445652	3.591447
REREP2Y	pseudogene	-1.000000	-1.000000	100.000000	97.795341	97.840481
AC024067.1	pseudogene	-1.000000	-1.000000	100.000000	-1.000000	100.000000