Parameters
input_file: 20090724_LUd4_7_hg19_ensembl59_S_iCLIP_TIAL1_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: 272161
[x-link sites] used in any map: 81457 (29.93%)
[single hits (=G+T), cDNA counts] total: 272161
[single hits (=G+T), cDNA counts] used in any map: 90979 (30.54%)

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	25455	9.35%	31.25%	26751	8.98%	29.40%
intron-exon	-300; 300	19252	7.07%	23.63%	20400	6.85%	22.42%
5-ncRNA	-1000; 300	4077	1.50%	5.01%	5480	1.84%	6.02%
ncRNA-3	-300; 1000	4709	1.73%	5.78%	6829	2.29%	7.51%
ORF-3UTR	-300; 300	11170	4.10%	13.71%	12741	4.28%	14.00%
5UTR-ORF	-300; 300	463	0.17%	0.57%	484	0.16%	0.53%
inter-5UTR	-1000; 300	948	0.35%	1.16%	1041	0.35%	1.14%
3UTR-inter	-300; 1000	11545	4.24%	14.17%	13097	4.40%	14.40%
inter-5	-1000; 300	3423	1.26%	4.20%	3955	1.33%	4.35%
3-inter	-300; 1000	15557	5.72%	19.10%	19167	6.43%	21.07%
BP best in intron	-300; 100	10741	3.95%	13.19%	11175	3.75%	12.28%

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	24819	9.12%	30.47%	97.50%	17463	1.39011
anti	636	0.23%	0.78%	2.50%	449	0.0356223
both	25455	9.35%	31.25%	100.00%	17854	1.42573
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	26001	8.73%	28.58%	97.20%	17463	1.45631
anti	750	0.25%	0.82%	2.80%	449	0.0420074
both	26751	8.98%	29.40%	100.00%	17854	1.49832

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; 71	0; 149
chr7:128411528@+	-300; 107	CALU	39; 0	84; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 33	0; 42
chr3:41281934@+	-300; 300	CTNNB1	29; 0	45; 0
chr2:191800015@+	-300; 300	GLS	26; 0	29; 0
chr6:18225699@-	-124; 192	DEK	24; 0	26; 0
chr12:50158717@+	-300; 300	TMBIM6	21; 0	33; 0
chr5:147650475@+	-75; 300	SPINK5L3	20; 0	24; 0
chr5:179048241@-	-78; 103	HNRNPH1	19; 0	30; 0
chr5:10401598@+	-300; 185	MARCH6	19; 0	27; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 71	0; 149
chr7:128411528@+	-300; 107	CALU	39; 0	84; 0
chr3:41281934@+	-300; 300	CTNNB1	29; 0	45; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 33	0; 42
chr12:50158717@+	-300; 300	TMBIM6	21; 0	33; 0
chr5:179048241@-	-78; 103	HNRNPH1	19; 0	30; 0
chr1:165624857@+	-127; 300	MGST3	15; 0	30; 0
chr2:191800015@+	-300; 300	GLS	26; 0	29; 0
chr5:10401598@+	-300; 185	MARCH6	19; 0	27; 0
chr6:18225699@-	-124; 192	DEK	24; 0	26; 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	18610	6.84%	22.85%	96.67%	13464	1.33491
anti	642	0.24%	0.79%	3.33%	518	0.0460512
both	19252	7.07%	23.63%	100.00%	13941	1.38096
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	19726	6.62%	21.68%	96.70%	13464	1.41496
anti	674	0.23%	0.74%	3.30%	518	0.0483466
both	20400	6.85%	22.42%	100.00%	13941	1.46331

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)
chr15:45009804@+	-300; 277	B2M	69; 0	125; 0
chr9:131456919@+	-292; 300	SET	53; 0	119; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	45; 0	58; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	97; 0
chr17:1248792@-	-300; 300	YWHAE	29; 0	52; 0
chr8:128753204@+	-241; 235	MYC	26; 0	49; 0
chr2:47387942@-	-300; 300	CALM2	26; 0	39; 0
chr10:112657785@+	-300; 300	PDCD4	24; 0	37; 0
chr1:165697357@-	-300; 292	TMCO1	23; 0	34; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	28; 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)
chr15:45009804@+	-300; 277	B2M	69; 0	125; 0
chr9:131456919@+	-292; 300	SET	53; 0	119; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	97; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	45; 0	58; 0
chr17:1248792@-	-300; 300	YWHAE	29; 0	52; 0
chr8:128753204@+	-241; 235	MYC	26; 0	49; 0
chr2:47387942@-	-300; 300	CALM2	26; 0	39; 0
chr10:112657785@+	-300; 300	PDCD4	24; 0	37; 0
chr1:165697357@-	-300; 292	TMCO1	23; 0	34; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	28; 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	1984	0.73%	2.44%	48.66%	832	1.05983
anti	2093	0.77%	2.57%	51.34%	1070	1.11806
both	4077	1.50%	5.01%	100.00%	1872	2.17788
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	3224	1.08%	3.54%	58.83%	832	1.72222
anti	2256	0.76%	2.48%	41.17%	1070	1.20513
both	5480	1.84%	6.02%	100.00%	1872	2.92735

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	480; 0	1321; 0
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chrUn_gl000220:109077@+	-758; 300	18S	47; 0	90; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr17:57918626@+	-338; 36	hsa-mir-21	40; 0	98; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 29	0; 39
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34
chr6:72113323@-	-1000; 35	C6orf155, hsa-mir-30a	27; 0	34; 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)
chr11:65269806@+	-1000; 29	MALAT1	480; 0	1321; 0
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chr17:57918626@+	-338; 36	hsa-mir-21	40; 0	98; 0
chrUn_gl000220:109077@+	-758; 300	18S	47; 0	90; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	15; 0	62; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 29	0; 39
chr6:72113323@-	-1000; 35	C6orf155, hsa-mir-30a	27; 0	34; 0

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	2970	1.09%	3.65%	63.07%	1231	1.39371
anti	1739	0.64%	2.13%	36.93%	934	0.816049
both	4709	1.73%	5.78%	100.00%	2131	2.20976
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	4975	1.67%	5.47%	72.85%	1231	2.33458
anti	1854	0.62%	2.04%	27.15%	934	0.870014
both	6829	2.29%	7.51%	100.00%	2131	3.2046

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	625; 0	1780; 0
chrUn_gl000220:110946@+	-300; 539	18S	64; 0	154; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	47; 0	159; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 37	0; 42
chr10:112658486@-	-300; 1000	NCRNA00081	0; 35	0; 48
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	29; 0	33; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 28	0; 36
chr8:128220109@-	-300; 1000	AC020688.1	25; 0	28; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 25	0; 34

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	625; 0	1780; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	47; 0	159; 0
chrUn_gl000220:110946@+	-300; 539	18S	64; 0	154; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	88; 0
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	16; 0	51; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 35	0; 48
chr15:65597130@+	-58; 1000	U5-ENSG00000200156	18; 0	44; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 37	0; 42
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	16; 0	41; 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	11003	4.04%	13.51%	98.50%	3199	3.34539
anti	167	0.06%	0.21%	1.50%	117	0.0507753
both	11170	4.10%	13.71%	100.00%	3289	3.39617
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	12566	4.22%	13.81%	98.63%	3199	3.82061
anti	175	0.06%	0.19%	1.37%	117	0.0532077
both	12741	4.28%	14.00%	100.00%	3289	3.87382

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)
chr19:13054727@+	-101; 288	CALR	92; 0	184; 0
chr3:149087560@-	-53; 300	TM4SF1	62; 0	106; 0
chr14:62213803@+	-76; 300	HIF1A	53; 0	82; 0
chr5:179156650@+	-145; 300	CANX	50; 0	73; 0
chr10:102120690@+	-100; 300	SCD	45; 0	62; 0
chr21:27253823@-	-129; 300	APP	42; 0	57; 0
chr7:148700882@-	-209; 300	PDIA4	40; 0	77; 0
chr1:35650053@-	-70; 300	SFPQ	40; 0	69; 0
chr7:6501391@-	-300; 300	KDELR2	38; 0	43; 0
chr1:156109094@+	-112; 233	LMNA	38; 0	51; 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)
chr19:13054727@+	-101; 288	CALR	92; 0	184; 0
chr3:149087560@-	-53; 300	TM4SF1	62; 0	106; 0
chr17:4849191@-	-50; 123	PFN1	35; 0	89; 0
chr14:62213803@+	-76; 300	HIF1A	53; 0	82; 0
chr7:148700882@-	-209; 300	PDIA4	40; 0	77; 0
chr5:179156650@+	-145; 300	CANX	50; 0	73; 0
chr1:35650053@-	-70; 300	SFPQ	40; 0	69; 0
chr10:102120690@+	-100; 300	SCD	45; 0	62; 0
chr21:27253823@-	-129; 300	APP	42; 0	57; 0
chr1:156109094@+	-112; 233	LMNA	38; 0	51; 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	393	0.14%	0.48%	84.88%	268	1.33673
anti	70	0.03%	0.09%	15.12%	29	0.238095
both	463	0.17%	0.57%	100.00%	294	1.57483
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	406	0.14%	0.45%	83.88%	268	1.38095
anti	78	0.03%	0.09%	16.12%	29	0.265306
both	484	0.16%	0.53%	100.00%	294	1.64626

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 21
chr7:135612307@+	-300; 127	AC015987.2	0; 13	0; 14
chr8:101733810@-	-252; 96	PABPC1	11; 0	11; 0
chr6:24718895@-	-300; 64	C6orf62	9; 0	11; 0
chr17:43226557@+	-300; 300	HEXIM1	7; 1	8; 1
chr5:138643104@+	-89; 300	MATR3	6; 0	7; 0
chr17:4851688@-	-300; 66	PFN1	6; 0	6; 0
chr14:24408733@+	-300; 99	C14orf167	0; 6	0; 6
chr11:3012265@+	-300; 90	AC131971.1	0; 6	0; 6
chr2:136873508@-	-152; 300	CXCR4	5; 0	5; 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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 21
chr7:135612307@+	-300; 127	AC015987.2	0; 13	0; 14
chr8:101733810@-	-252; 96	PABPC1	11; 0	11; 0
chr6:24718895@-	-300; 64	C6orf62	9; 0	11; 0
chr17:43226557@+	-300; 300	HEXIM1	7; 1	8; 1
chr5:138643104@+	-89; 300	MATR3	6; 0	7; 0
chr17:4851688@-	-300; 66	PFN1	6; 0	6; 0
chr14:24408733@+	-300; 99	C14orf167	0; 6	0; 6
chr11:3012265@+	-300; 90	AC131971.1	0; 6	0; 6
chr22:38884251@-	-142; 187	DDX17	4; 0	5; 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	285	0.10%	0.35%	30.06%	197	0.467213
anti	663	0.24%	0.81%	69.94%	429	1.08689
both	948	0.35%	1.16%	100.00%	610	1.5541
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	312	0.10%	0.34%	29.97%	197	0.511475
anti	729	0.24%	0.80%	70.03%	429	1.19508
both	1041	0.35%	1.14%	100.00%	610	1.70656

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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr8:101734314@-	-1000; 252	PABPC1	26; 0	46; 0
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 17	0; 22
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 16
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 12
chr5:147647742@+	-1000; 164	SPINK5L3	10; 0	10; 0
chr7:26240781@+	-1000; 200	CBX3	0; 9	0; 10
chr5:32788944@+	-844; 281	C5orf23	9; 0	10; 0
chr5:175815975@-	-1000; 188	NOP16	0; 7	0; 8
chr8:33370702@-	-1000; 286	C8orf41	0; 6	0; 7

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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr8:101734314@-	-1000; 252	PABPC1	26; 0	46; 0
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 17	0; 22
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 16
chr13:41635409@+	-1000; 200	WBP4	0; 3	0; 12
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 12
chr7:26240781@+	-1000; 200	CBX3	0; 9	0; 10
chr5:147647742@+	-1000; 164	SPINK5L3	10; 0	10; 0
chr5:32788944@+	-844; 281	C5orf23	9; 0	10; 0
chr5:175815975@-	-1000; 188	NOP16	0; 7	0; 8

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	10008	3.68%	12.29%	86.69%	3266	2.71146
anti	1537	0.56%	1.89%	13.31%	579	0.416418
both	11545	4.24%	14.17%	100.00%	3691	3.12788
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	11304	3.79%	12.42%	86.31%	3266	3.06258
anti	1793	0.60%	1.97%	13.69%	579	0.485776
both	13097	4.40%	14.40%	100.00%	3691	3.54836

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; 72	0; 116
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chr16:18802989@-	-300; 667	ARL6IP1	47; 0	62; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 42	1; 58
chr22:38879452@+	-263; 1000	KDELR3	0; 40	0; 45
chr19:57805436@+	-300; 1000	ZNF460	39; 0	41; 0
chr12:104744062@+	-300; 1000	TXNRD1	39; 0	54; 0
chr16:87863620@-	-300; 1000	SLC7A5	37; 0	62; 0
chr12:20833881@+	-300; 1000	PDE3A	36; 0	44; 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; 72	0; 116
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 89
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chr16:87863620@-	-300; 1000	SLC7A5	37; 0	62; 0
chr16:18802989@-	-300; 667	ARL6IP1	47; 0	62; 0
chr17:79845715@-	-144; 1000	THOC4	24; 0	61; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 42	1; 58
chr12:104744062@+	-300; 1000	TXNRD1	39; 0	54; 0
chr19:39327027@-	-166; 1000	HNRNPL	30; 0	53; 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	909	0.33%	1.12%	26.56%	523	0.497265
anti	2514	0.92%	3.09%	73.44%	1344	1.37527
both	3423	1.26%	4.20%	100.00%	1828	1.87254
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	1127	0.38%	1.24%	28.50%	523	0.616521
anti	2828	0.95%	3.11%	71.50%	1344	1.54705
both	3955	1.33%	4.35%	100.00%	1828	2.16357

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)
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 67	0; 150
chrUn_gl000220:109077@+	-758; 300	18S	47; 0	90; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 29	0; 39
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34
chr8:101734314@-	-1000; 252	PABPC1	26; 0	46; 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)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 67	0; 150
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chrUn_gl000220:109077@+	-758; 300	18S	47; 0	90; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	15; 0	62; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr8:101734314@-	-1000; 252	PABPC1	26; 0	46; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 29	0; 39

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	12494	4.59%	15.34%	80.31%	4061	2.4498
anti	3063	1.13%	3.76%	19.69%	1238	0.600588
both	15557	5.72%	19.10%	100.00%	5100	3.05039
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	15676	5.26%	17.23%	81.79%	4061	3.07373
anti	3491	1.17%	3.84%	18.21%	1238	0.68451
both	19167	6.43%	21.07%	100.00%	5100	3.75824

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	625; 0	1780; 0
chr1:169101767@-	-127; 1000	NME7	1; 91	1; 139
chr19:39220830@-	-300; 1000	CAPN12	0; 72	0; 116
chr7:5566780@-	-300; 1000	ACTB	68; 0	220; 0
chrUn_gl000220:110946@+	-300; 539	18S	64; 0	154; 0
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr16:18802989@-	-300; 667	ARL6IP1	47; 0	62; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 42	1; 58

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	625; 0	1780; 0
chr7:5566780@-	-300; 1000	ACTB	68; 0	220; 0
chrUn_gl000220:110946@+	-300; 539	18S	64; 0	154; 0
chr1:169101767@-	-127; 1000	NME7	1; 91	1; 139
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 72	0; 116
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 89
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	88; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 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	10306	3.79%	12.65%	95.95%	8236	1.20173
anti	435	0.16%	0.53%	4.05%	358	0.0507229
both	10741	3.95%	13.19%	100.00%	8576	1.25245
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	10727	3.60%	11.79%	95.99%	8236	1.25082
anti	448	0.15%	0.49%	4.01%	358	0.0522388
both	11175	3.75%	12.28%	100.00%	8576	1.30306

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)
chr5:179045370@-	-300; 47	HNRNPH1	20; 0	22; 0
chr5:147653879@+	-300; 28	SPINK5L3	18; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	18; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	15; 0	15; 0
chr16:31199583@+	-300; 60	FUS	15; 0	16; 0
chr2:61413393@+	-229; 100	AHSA2	14; 0	17; 0
chr1:1326494@-	-300; 100	CCNL2	13; 0	15; 0
chr5:179046653@-	-300; 100	HNRNPH1	12; 0	15; 0
chr5:179048854@-	-300; 100	HNRNPH1	11; 0	13; 0
chr16:277586@-	-300; 100	LUC7L	11; 0	11; 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	10; 0	33; 0
chr5:179045370@-	-300; 47	HNRNPH1	20; 0	22; 0
chr5:147653879@+	-300; 28	SPINK5L3	18; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	18; 0
chr2:61413393@+	-229; 100	AHSA2	14; 0	17; 0
chr16:31199583@+	-300; 60	FUS	15; 0	16; 0
chr1:28835317@+	-300; 22	SNHG3	9; 0	16; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	15; 0	15; 0
chr5:179046653@-	-300; 100	HNRNPH1	12; 0	15; 0
chr1:1326494@-	-300; 100	CCNL2	13; 0	15; 0

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