Parameters
input_file: 20090724_LUd4_4_hg19_ensembl59_G_iCLIP_TIA1_HeLa_bedGraph-cDNA-hits-in-genome.bed.gz
input_res_type: single hits in whole-genome, cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 6742
[x-link sites] used in any map: 2074 (30.76%)
[single hits in whole-genome, cDNA counts] total: 6742
[single hits in whole-genome, cDNA counts] used in any map: 2151 (30.39%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map
exon-intron	-300; 300	524	7.77%	25.27%	543	7.67%	25.24%
intron-exon	-300; 300	405	6.01%	19.53%	419	5.92%	19.48%
5-ncRNA	-1000; 300	128	1.90%	6.17%	133	1.88%	6.18%
ncRNA-3	-300; 1000	160	2.37%	7.71%	170	2.40%	7.90%
ORF-3UTR	-300; 300	362	5.37%	17.45%	376	5.31%	17.48%
5UTR-ORF	-300; 300	7	0.10%	0.34%	9	0.13%	0.42%
inter-5UTR	-1000; 300	27	0.40%	1.30%	29	0.41%	1.35%
3UTR-inter	-300; 1000	406	6.02%	19.58%	415	5.86%	19.29%
inter-5	-1000; 300	111	1.65%	5.35%	118	1.67%	5.49%
3-inter	-300; 1000	536	7.95%	25.84%	555	7.84%	25.80%
BP best in intron	-300; 100	190	2.82%	9.16%	196	2.77%	9.11%

Download statistics in tab-delimited format.
Download graphs in tab-delimited format.

RNAmap exon-intron

junction is at position zero.
upstream is regions of type: ORF, 3UTR, 5UTR
downstream is regions of type: intron

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	503	7.46%	24.25%	95.99%	473	1.03074
anti	21	0.31%	1.01%	4.01%	15	0.0430328
both	524	7.77%	25.27%	100.00%	488	1.07377
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	519	7.33%	24.13%	95.58%	473	1.06352
anti	24	0.34%	1.12%	4.42%	15	0.0491803
both	543	7.67%	25.24%	100.00%	488	1.1127

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 7	0; 7
chr7:128411528@+	-300; 107	CALU	5; 0	5; 0
chr3:41281934@+	-300; 300	CTNNB1	4; 0	4; 0
chr5:142660683@-	-300; 300	NR3C1	3; 0	3; 0
chrX:154307205@+	-92; 300	BRCC3	2; 0	2; 0
chr7:65670509@+	-95; 135	TPST1	2; 0	2; 0
chr6:74513024@+	-41; 300	CD109	2; 0	2; 0
chr5:71591356@-	-30; 300	MRPS27	2; 0	2; 0
chr5:38935743@+	-300; 300	OSMR	2; 0	2; 0
chr3:111651244@+	-65; 300	PHLDB2	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 7	0; 7
chr7:128411528@+	-300; 107	CALU	5; 0	5; 0
chr3:41281934@+	-300; 300	CTNNB1	4; 0	4; 0
chr5:142660683@-	-300; 300	NR3C1	3; 0	3; 0
chr22:18189591@+	-58; 300	BCL2L13	2; 0	3; 0
chr2:179410113@-	-153; 300	TTN	0; 1	0; 3
chr19:17513754@-	-189; 300	BST2	2; 0	3; 0
chrX:154307205@+	-92; 300	BRCC3	2; 0	2; 0
chr8:119945168@-	-185; 300	TNFRSF11B	1; 0	2; 0
chr8:62596596@-	-75; 300	ASPH	1; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap intron-exon

junction is at position zero.
upstream is regions of type: intron
downstream is regions of type: ORF, 3UTR, 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	390	5.78%	18.80%	96.30%	359	1.04839
anti	15	0.22%	0.72%	3.70%	13	0.0403226
both	405	6.01%	19.53%	100.00%	372	1.08871
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	403	5.69%	18.74%	96.18%	359	1.08333
anti	16	0.23%	0.74%	3.82%	13	0.0430108
both	419	5.92%	19.48%	100.00%	372	1.12634

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	8; 0	12; 0
chr7:112415372@-	-300; 71	TMEM168	4; 0	4; 0
chrX:107408267@-	-166; 81	COL4A6	0; 2	0; 2
chr9:33116110@-	-300; 61	B4GALT1	2; 0	2; 0
chr9:75784966@+	-300; 171	ANXA1	2; 0	2; 0
chr8:128753204@+	-241; 235	MYC	2; 0	2; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	2; 0	2; 0
chr7:6502805@-	-300; 300	KDELR2	2; 0	2; 0
chr6:131225679@-	-300; 38	EPB41L2	2; 0	2; 0
chr6:3737429@-	-300; 59	C6orf145	2; 0	3; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	8; 0	12; 0
chr7:112415372@-	-300; 71	TMEM168	4; 0	4; 0
chr6:3737429@-	-300; 59	C6orf145	2; 0	3; 0
chr17:30226748@-	-300; 42	UTP6	0; 2	0; 3
chrX:107408267@-	-166; 81	COL4A6	0; 2	0; 2
chr9:33116110@-	-300; 61	B4GALT1	2; 0	2; 0
chr9:75784966@+	-300; 171	ANXA1	2; 0	2; 0
chr8:128753204@+	-241; 235	MYC	2; 0	2; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	2; 0	2; 0
chr7:6502805@-	-300; 300	KDELR2	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5-ncRNA

junction is at position zero.
upstream is regions of type: intron, inter, telo
downstream is regions of type: ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	61	0.90%	2.94%	47.66%	31	0.677778
anti	67	0.99%	3.23%	52.34%	59	0.744444
both	128	1.90%	6.17%	100.00%	90	1.42222
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	62	0.88%	2.88%	46.62%	31	0.688889
anti	71	1.00%	3.30%	53.38%	59	0.788889
both	133	1.88%	6.18%	100.00%	90	1.47778

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	21; 0	22; 0
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 3	0; 3
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 3	0; 4
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	2; 0	2; 0
chr21:16333629@+	-1000; 206	AF127577.10	0; 2	0; 2
chr2:70315685@-	-1000; 62	AC136007.2	0; 2	0; 2
chr14:69926227@-	-1000; 300	AL157996.1	0; 2	0; 2
chr1:205685227@+	-1000; 300	AC119673.2	0; 2	0; 3

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	21; 0	22; 0
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 3	0; 4
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 3	0; 3
chr1:205685227@+	-1000; 300	AC119673.2	0; 2	0; 3
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	2; 0	2; 0
chr21:16333629@+	-1000; 206	AF127577.10	0; 2	0; 2
chr2:70315685@-	-1000; 62	AC136007.2	0; 2	0; 2
chr17:2577028@-	-1000; 300	AC005696.2	0; 1	0; 2

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ncRNA-3

junction is at position zero.
upstream is regions of type: ncRNA
downstream is regions of type: intron, inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	132	1.96%	6.36%	82.50%	88	1.14783
anti	28	0.42%	1.35%	17.50%	27	0.243478
both	160	2.37%	7.71%	100.00%	115	1.3913
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	141	1.99%	6.56%	82.94%	88	1.22609
anti	29	0.41%	1.35%	17.06%	27	0.252174
both	170	2.40%	7.90%	100.00%	115	1.47826

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	3; 0	3; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	3; 0	3; 0
chr1:224051426@-	-300; 1000	ACTBP11	3; 0	3; 0
chr9:35657749@-	-132; 1000	RNase_MRP-ENSG00000199916	2; 0	2; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 2	0; 2
chr5:77081268@+	-282; 1000	CTD-2309M13.1	2; 0	2; 0
chr3:175695283@-	-300; 1000	RP11-809F4.2	2; 0	2; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	3; 0	3; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	3; 0	3; 0
chr4:52731214@-	-243; 1000	RP11-365H22.1	1; 0	3; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	2; 0	3; 0
chr1:224051426@-	-300; 1000	ACTBP11	3; 0	3; 0
chrX:118557868@+	-82; 1000	SLC25A43, U1-ENSG00000207175	1; 0	2; 0
chr9:35657749@-	-132; 1000	RNase_MRP-ENSG00000199916	2; 0	2; 0
chr8:98737113@-	-300; 1000	AP003357.3	0; 1	0; 2

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ORF-3UTR

junction is at position zero.
upstream is regions of type: ORF
downstream is regions of type: 3UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	359	5.32%	17.31%	99.17%	276	1.28674
anti	3	0.04%	0.14%	0.83%	3	0.0107527
both	362	5.37%	17.45%	100.00%	279	1.29749
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	373	5.27%	17.34%	99.20%	276	1.33692
anti	3	0.04%	0.14%	0.80%	3	0.0107527
both	376	5.31%	17.48%	100.00%	279	1.34767

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr3:149087560@-	-53; 300	TM4SF1	9; 0	10; 0
chr22:38881684@-	-300; 300	DDX17	9; 0	10; 0
chr12:120899818@-	-73; 174	SFRS9	6; 0	6; 0
chr5:179156650@+	-145; 300	CANX	5; 0	5; 0
chr3:50099031@+	-69; 181	RBM6	5; 0	5; 0
chr7:148700882@-	-209; 300	PDIA4	4; 0	5; 0
chr5:122359566@-	-66; 300	PPIC	4; 0	4; 0
chr2:189876774@+	-211; 300	COL3A1	4; 0	5; 0
chr17:30696778@+	-81; 300	ZNF207	4; 0	4; 0
chr1:35650053@-	-70; 300	SFPQ	4; 0	4; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr3:149087560@-	-53; 300	TM4SF1	9; 0	10; 0
chr22:38881684@-	-300; 300	DDX17	9; 0	10; 0
chr12:120899818@-	-73; 174	SFRS9	6; 0	6; 0
chr7:148700882@-	-209; 300	PDIA4	4; 0	5; 0
chr5:179156650@+	-145; 300	CANX	5; 0	5; 0
chr3:50099031@+	-69; 181	RBM6	5; 0	5; 0
chr2:189876774@+	-211; 300	COL3A1	4; 0	5; 0
chr5:122359566@-	-66; 300	PPIC	4; 0	4; 0
chr17:30696778@+	-81; 300	ZNF207	4; 0	4; 0
chr1:35650053@-	-70; 300	SFPQ	4; 0	4; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5UTR-ORF

junction is at position zero.
upstream is regions of type: 5UTR
downstream is regions of type: ORF

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	6	0.09%	0.29%	85.71%	6	0.857143
anti	1	0.01%	0.05%	14.29%	1	0.142857
both	7	0.10%	0.34%	100.00%	7	1
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	8	0.11%	0.37%	88.89%	6	1.14286
anti	1	0.01%	0.05%	11.11%	1	0.142857
both	9	0.13%	0.42%	100.00%	7	1.28571

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:111196308@+	-168; 55	AMD1	1; 0	1; 0
chr6:1390182@+	-57; 300	FOXF2	1; 0	2; 0
chr5:132161831@-	-224; 300	SHROOM1	1; 0	1; 0
chr4:103747792@-	-243; 76	UBE2D3	1; 0	1; 0
chr19:49468764@+	-100; 51	FTL	1; 0	1; 0
chr17:43226557@+	-300; 300	HEXIM1	1; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr6:1390182@+	-57; 300	FOXF2	1; 0	2; 0
chr17:43226557@+	-300; 300	HEXIM1	1; 0	2; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:111196308@+	-168; 55	AMD1	1; 0	1; 0
chr5:132161831@-	-224; 300	SHROOM1	1; 0	1; 0
chr4:103747792@-	-243; 76	UBE2D3	1; 0	1; 0
chr19:49468764@+	-100; 51	FTL	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5UTR

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	10	0.15%	0.48%	37.04%	10	0.37037
anti	17	0.25%	0.82%	62.96%	17	0.62963
both	27	0.40%	1.30%	100.00%	27	1
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	12	0.17%	0.56%	41.38%	10	0.444444
anti	17	0.24%	0.79%	58.62%	17	0.62963
both	29	0.41%	1.35%	100.00%	27	1.07407

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrX:108976631@-	-1000; 64	ACSL4	0; 1	0; 1
chr6:151773315@-	-1000; 83	RMND1	0; 1	0; 1
chr6:166401114@+	-1000; 249	AL132661.1	0; 1	0; 1
chr6:27805537@+	-1000; 300	HIST1H2BN	1; 0	1; 0
chr5:140071608@-	-1000; 300	HARS	0; 1	0; 1
chr5:443257@-	-1000; 160	C5orf55	0; 1	0; 1
chr5:139944040@+	-1000; 54	SLC35A4	0; 1	0; 1
chr5:32788944@+	-844; 281	C5orf23	1; 0	1; 0
chr4:77997141@-	-1000; 184	CCNI	1; 0	1; 0
chr2:228029265@-	-1000; 272	COL4A4	0; 1	0; 1

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr15:77544872@-	-1000; 82	AC107883.1	1; 0	2; 0
chr12:21654698@+	-1000; 79	GOLT1B	1; 0	2; 0
chrX:108976631@-	-1000; 64	ACSL4	0; 1	0; 1
chr6:151773315@-	-1000; 83	RMND1	0; 1	0; 1
chr6:166401114@+	-1000; 249	AL132661.1	0; 1	0; 1
chr6:27805537@+	-1000; 300	HIST1H2BN	1; 0	1; 0
chr5:140071608@-	-1000; 300	HARS	0; 1	0; 1
chr5:443257@-	-1000; 160	C5orf55	0; 1	0; 1
chr5:139944040@+	-1000; 54	SLC35A4	0; 1	0; 1
chr5:32788944@+	-844; 281	C5orf23	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3UTR-inter

junction is at position zero.
upstream is regions of type: 3UTR
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	357	5.30%	17.21%	87.93%	288	1.09846
anti	49	0.73%	2.36%	12.07%	37	0.150769
both	406	6.02%	19.58%	100.00%	325	1.24923
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	365	5.16%	16.97%	87.95%	288	1.12308
anti	50	0.71%	2.32%	12.05%	37	0.153846
both	415	5.86%	19.29%	100.00%	325	1.27692

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:39220830@-	-300; 1000	CAPN12	0; 7	0; 8
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr17:79845715@-	-144; 1000	THOC4	4; 0	4; 0
chr15:65255360@-	-299; 1000	SPG21	4; 0	4; 0
chr15:45010359@+	-278; 1000	B2M	4; 0	4; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 4	0; 4
chr8:131064351@-	-300; 1000	ASAP1	3; 0	3; 0
chr21:44834393@-	-300; 1000	SIK1	3; 0	3; 0
chr2:20232409@-	-260; 1000	LAPTM4A	3; 0	3; 0
chr17:40465340@-	-300; 1000	STAT3	3; 0	3; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:39220830@-	-300; 1000	CAPN12	0; 7	0; 8
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr17:79845715@-	-144; 1000	THOC4	4; 0	4; 0
chr17:4848945@-	-123; 1000	PFN1	2; 0	4; 0
chr15:65255360@-	-299; 1000	SPG21	4; 0	4; 0
chr15:45010359@+	-278; 1000	B2M	4; 0	4; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 4	0; 4
chr8:131064351@-	-300; 1000	ASAP1	3; 0	3; 0
chr21:44834393@-	-300; 1000	SIK1	3; 0	3; 0
chr2:20232409@-	-260; 1000	LAPTM4A	3; 0	3; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	29	0.43%	1.40%	26.13%	24	0.305263
anti	82	1.22%	3.95%	73.87%	71	0.863158
both	111	1.65%	5.35%	100.00%	95	1.16842
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	31	0.44%	1.44%	26.27%	24	0.326316
anti	87	1.23%	4.04%	73.73%	71	0.915789
both	118	1.67%	5.49%	100.00%	95	1.24211

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 3	0; 3
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 3	0; 3
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 3	0; 4
chr9:131037657@+	-1000; 59	C9orf119	0; 2	0; 3
chr7:45023783@-	-596; 148	C7orf40	2; 0	2; 0
chr21:16333629@+	-1000; 206	AF127577.10	0; 2	0; 2
chr2:70315685@-	-1000; 62	AC136007.2	0; 2	0; 2
chr14:69926227@-	-1000; 300	AL157996.1	0; 2	0; 2
chr1:205685227@+	-1000; 300	AC119673.2	0; 2	0; 3

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 3	0; 4
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 3	0; 3
chr9:131037657@+	-1000; 59	C9orf119	0; 2	0; 3
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 3	0; 3
chr1:205685227@+	-1000; 300	AC119673.2	0; 2	0; 3
chr7:45023783@-	-596; 148	C7orf40	2; 0	2; 0
chr21:16333629@+	-1000; 206	AF127577.10	0; 2	0; 2
chr2:70315685@-	-1000; 62	AC136007.2	0; 2	0; 2
chr17:2577028@-	-1000; 300	AC005696.2	0; 1	0; 2

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3-inter

junction is at position zero.
upstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	460	6.82%	22.18%	85.82%	346	1.13022
anti	76	1.13%	3.66%	14.18%	61	0.186732
both	536	7.95%	25.84%	100.00%	407	1.31695
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	476	6.73%	22.13%	85.77%	346	1.16953
anti	79	1.12%	3.67%	14.23%	61	0.194103
both	555	7.84%	25.80%	100.00%	407	1.36364

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 7	0; 8
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr17:79845715@-	-144; 1000	THOC4	4; 0	4; 0
chr15:65255360@-	-299; 1000	SPG21	4; 0	4; 0
chr15:45010359@+	-278; 1000	B2M	4; 0	4; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 4	0; 4
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chr8:131064351@-	-300; 1000	ASAP1	3; 0	3; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	3; 0	3; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 7	0; 8
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr17:79845715@-	-144; 1000	THOC4	4; 0	4; 0
chr17:4848945@-	-123; 1000	PFN1	2; 0	4; 0
chr15:65255360@-	-299; 1000	SPG21	4; 0	4; 0
chr15:45010359@+	-278; 1000	B2M	4; 0	4; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 4	0; 4
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chr8:131064351@-	-300; 1000	ASAP1	3; 0	3; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap "BP best in intron"

BP is at position zero.
upstream is usptream of branch point
downstream is downstream of branch point

[eps]

x-links and BPs distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [BPs] in map	[x-link sites] per unique [BP]
same	182	2.70%	8.78%	95.79%	177	0.98913
anti	8	0.12%	0.39%	4.21%	7	0.0434783
both	190	2.82%	9.16%	100.00%	184	1.03261
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [BPs] in map	[single hits in whole-genome, cDNA counts] per unique [BP]
same	188	2.66%	8.74%	95.92%	177	1.02174
anti	8	0.11%	0.37%	4.08%	7	0.0434783
both	196	2.77%	9.11%	100.00%	184	1.06522

Top 10 BPs with largest x-link sites sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrX:107408303@-	-130; 36	COL4A6	0; 2	0; 2
chr9:86584384@-	-300; 90	HNRNPK	2; 0	3; 0
chr6:131225751@-	-300; 72	EPB41L2	2; 0	2; 0
chr6:3737462@-	-300; 33	C6orf145	2; 0	3; 0
chr5:6632134@-	-266; 45	NSUN2	2; 0	2; 0
chr17:62496969@-	-300; 79	DDX5	2; 0	2; 0
chrX:85156461@-	-300; 100	CHM	1; 0	1; 0
chrX:53641728@-	-300; 23	HUWE1	1; 0	1; 0
chrX:107377261@+	-300; 23	ATG4A	1; 0	1; 0
chrX:44896868@+	-300; 29	KDM6A	1; 0	1; 0

Top 10 BPs with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr9:86584384@-	-300; 90	HNRNPK	2; 0	3; 0
chr6:3737462@-	-300; 33	C6orf145	2; 0	3; 0
chrX:107408303@-	-130; 36	COL4A6	0; 2	0; 2
chr6:131225751@-	-300; 72	EPB41L2	2; 0	2; 0
chr6:133785763@+	-300; 100	EYA4	1; 0	2; 0
chr5:6632134@-	-266; 45	NSUN2	2; 0	2; 0
chr3:112269438@-	-300; 100	ATG3	1; 0	2; 0
chr17:62496969@-	-300; 79	DDX5	2; 0	2; 0
chr17:2577248@+	-300; 100	PAFAH1B1	1; 0	2; 0
chr12:939010@+	-300; 100	WNK1	1; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.