Parameters
input_file: 20090724_LUd4_4_hg19_ensembl59_S_iCLIP_TIA1_HeLa_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), 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: 7189
[x-link sites] used in any map: 2165 (30.12%)
[single hits (=G+T), cDNA counts] total: 7189
[single hits (=G+T), cDNA counts] used in any map: 2246 (29.68%)

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 (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	536	7.46%	24.76%	559	7.39%	24.89%
intron-exon	-300; 300	423	5.88%	19.54%	437	5.77%	19.46%
5-ncRNA	-1000; 300	134	1.86%	6.19%	139	1.84%	6.19%
ncRNA-3	-300; 1000	175	2.43%	8.08%	185	2.44%	8.24%
ORF-3UTR	-300; 300	377	5.24%	17.41%	391	5.17%	17.41%
5UTR-ORF	-300; 300	7	0.10%	0.32%	9	0.12%	0.40%
inter-5UTR	-1000; 300	31	0.43%	1.43%	33	0.44%	1.47%
3UTR-inter	-300; 1000	420	5.84%	19.40%	429	5.67%	19.10%
inter-5	-1000; 300	120	1.67%	5.54%	127	1.68%	5.65%
3-inter	-300; 1000	564	7.85%	26.05%	583	7.70%	25.96%
BP best in intron	-300; 100	198	2.75%	9.15%	204	2.70%	9.08%

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	509	7.08%	23.51%	94.96%	479	1.02209
anti	27	0.38%	1.25%	5.04%	19	0.0542169
both	536	7.46%	24.76%	100.00%	498	1.07631
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	525	6.94%	23.37%	93.92%	479	1.05422
anti	34	0.45%	1.51%	6.08%	19	0.0682731
both	559	7.39%	24.89%	100.00%	498	1.12249

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 (=G+T), 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
chr3:13918465@-	-126; 300	WNT7A	0; 2	0; 2

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 7	0; 7
chr7:128411528@+	-300; 107	CALU	5; 0	5; 0
chr22:30138405@-	-32; 300	ZMAT5	0; 2	0; 5
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

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	404	5.62%	18.66%	95.51%	367	1.05208
anti	19	0.26%	0.88%	4.49%	17	0.0494792
both	423	5.88%	19.54%	100.00%	384	1.10156
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	417	5.51%	18.57%	95.42%	367	1.08594
anti	20	0.26%	0.89%	4.58%	17	0.0520833
both	437	5.77%	19.46%	100.00%	384	1.13802

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 (=G+T), cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	13; 0	17; 0
chr7:112415372@-	-300; 71	TMEM168	4; 0	4; 0
chr2:47387942@-	-300; 300	CALM2	3; 0	3; 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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	13; 0	17; 0
chr7:112415372@-	-300; 71	TMEM168	4; 0	4; 0
chr6:3737429@-	-300; 59	C6orf145	2; 0	3; 0
chr2:47387942@-	-300; 300	CALM2	3; 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

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	64	0.89%	2.96%	47.76%	34	0.666667
anti	70	0.97%	3.23%	52.24%	62	0.729167
both	134	1.86%	6.19%	100.00%	96	1.39583
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	65	0.86%	2.89%	46.76%	34	0.677083
anti	74	0.98%	3.29%	53.24%	62	0.770833
both	139	1.84%	6.19%	100.00%	96	1.44792

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	145	2.02%	6.70%	82.86%	98	1.14173
anti	30	0.42%	1.39%	17.14%	29	0.23622
both	175	2.43%	8.08%	100.00%	127	1.37795
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	154	2.03%	6.86%	83.24%	98	1.2126
anti	31	0.41%	1.38%	16.76%	29	0.244094
both	185	2.44%	8.24%	100.00%	127	1.45669

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chrUn_gl000220:110946@+	-300; 539	18S	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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chrUn_gl000220:118417@+	-300; 1000	28S	3; 0	3; 0
chrUn_gl000220:110946@+	-300; 539	18S	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

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	374	5.20%	17.27%	99.20%	288	1.28522
anti	3	0.04%	0.14%	0.80%	3	0.0103093
both	377	5.24%	17.41%	100.00%	291	1.29553
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	388	5.13%	17.28%	99.23%	288	1.33333
anti	3	0.04%	0.13%	0.77%	3	0.0103093
both	391	5.17%	17.41%	100.00%	291	1.34364

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	0.08%	0.28%	85.71%	6	0.857143
anti	1	0.01%	0.05%	14.29%	1	0.142857
both	7	0.10%	0.32%	100.00%	7	1
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	8	0.11%	0.36%	88.89%	6	1.14286
anti	1	0.01%	0.04%	11.11%	1	0.142857
both	9	0.12%	0.40%	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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	12	0.17%	0.55%	38.71%	11	0.4
anti	19	0.26%	0.88%	61.29%	19	0.633333
both	31	0.43%	1.43%	100.00%	30	1.03333
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	14	0.18%	0.62%	42.42%	11	0.466667
anti	19	0.25%	0.85%	57.58%	19	0.633333
both	33	0.44%	1.47%	100.00%	30	1.1

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 (=G+T), cDNA counts] (same; anti)
chr8:101734314@-	-1000; 252	PABPC1	2; 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
chr4:77997141@-	-1000; 184	CCNI	1; 0	1; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
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

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	369	5.13%	17.04%	87.86%	297	1.10149
anti	51	0.71%	2.36%	12.14%	38	0.152239
both	420	5.84%	19.40%	100.00%	335	1.25373
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	377	4.98%	16.79%	87.88%	297	1.12537
anti	52	0.69%	2.32%	12.12%	38	0.155224
both	429	5.67%	19.10%	100.00%	335	1.2806

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 (=G+T), cDNA counts] (same; anti)
chr19:39220830@-	-300; 1000	CAPN12	0; 8	0; 9
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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr19:39220830@-	-300; 1000	CAPN12	0; 8	0; 9
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	34	0.47%	1.57%	28.33%	28	0.330097
anti	86	1.20%	3.97%	71.67%	75	0.834951
both	120	1.67%	5.54%	100.00%	103	1.16505
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	36	0.48%	1.60%	28.35%	28	0.349515
anti	91	1.20%	4.05%	71.65%	75	0.883495
both	127	1.68%	5.65%	100.00%	103	1.23301

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 (=G+T), 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
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
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

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	483	6.72%	22.31%	85.64%	362	1.13647
anti	81	1.13%	3.74%	14.36%	63	0.190588
both	564	7.85%	26.05%	100.00%	425	1.32706
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	499	6.59%	22.22%	85.59%	362	1.17412
anti	84	1.11%	3.74%	14.41%	63	0.197647
both	583	7.70%	25.96%	100.00%	425	1.37176

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 8	0; 9
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr6:44221831@-	-300; 1000	SLC35B2	0; 4	0; 5
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
chrUn_gl000220:110946@+	-300; 539	18S	3; 0	3; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	29; 0	33; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 8	0; 9
chr10:93625033@+	-300; 1000	TNKS2	6; 0	6; 0
chr6:44221831@-	-300; 1000	SLC35B2	0; 4	0; 5
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

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	185	2.57%	8.55%	93.43%	180	0.963542
anti	13	0.18%	0.60%	6.57%	12	0.0677083
both	198	2.75%	9.15%	100.00%	192	1.03125
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	191	2.52%	8.50%	93.63%	180	0.994792
anti	13	0.17%	0.58%	6.37%	12	0.0677083
both	204	2.70%	9.08%	100.00%	192	1.0625

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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.