Parameters
input_file: 20090724_LUd4_2_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: 146981
[x-link sites] used in any map: 48341 (32.89%)
[single hits (=G+T), cDNA counts] total: 146981
[single hits (=G+T), cDNA counts] used in any map: 54233 (33.75%)

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	14046	9.56%	29.06%	14776	9.19%	27.25%
intron-exon	-300; 300	10405	7.08%	21.52%	11046	6.87%	20.37%
5-ncRNA	-1000; 300	2389	1.63%	4.94%	3339	2.08%	6.16%
ncRNA-3	-300; 1000	2593	1.76%	5.36%	3399	2.12%	6.27%
ORF-3UTR	-300; 300	8291	5.64%	17.15%	9671	6.02%	17.83%
5UTR-ORF	-300; 300	252	0.17%	0.52%	269	0.17%	0.50%
inter-5UTR	-1000; 300	652	0.44%	1.35%	791	0.49%	1.46%
3UTR-inter	-300; 1000	7937	5.40%	16.42%	9006	5.60%	16.61%
inter-5	-1000; 300	2166	1.47%	4.48%	2726	1.70%	5.03%
3-inter	-300; 1000	10285	7.00%	21.28%	12155	7.56%	22.41%
BP best in intron	-300; 100	5598	3.81%	11.58%	5825	3.62%	10.74%

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	13723	9.34%	28.39%	97.70%	10731	1.25416
anti	323	0.22%	0.67%	2.30%	229	0.0295193
both	14046	9.56%	29.06%	100.00%	10942	1.28368
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	14391	8.95%	26.54%	97.39%	10731	1.31521
anti	385	0.24%	0.71%	2.61%	229	0.0351855
both	14776	9.19%	27.25%	100.00%	10942	1.35039

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; 37	0; 89
chr3:41281934@+	-300; 300	CTNNB1	23; 0	30; 0
chr12:50158717@+	-300; 300	TMBIM6	22; 0	31; 0
chr7:128411528@+	-300; 107	CALU	21; 0	31; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 18	1; 20
chr5:10401598@+	-300; 185	MARCH6	16; 0	23; 0
chr12:98928321@+	-101; 300	TMPO	12; 0	13; 0
chr8:22280254@+	-300; 300	SLC39A14	11; 0	12; 0
chr2:191800015@+	-300; 300	GLS	11; 0	12; 0
chr1:165624857@+	-127; 300	MGST3	11; 0	17; 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)
chr7:139025365@+	-85; 256	C7orf55	7; 0	98; 0
chr1:45976739@+	-281; 300	MMACHC	0; 37	0; 89
chr7:128411528@+	-300; 107	CALU	21; 0	31; 0
chr12:50158717@+	-300; 300	TMBIM6	22; 0	31; 0
chr3:41281934@+	-300; 300	CTNNB1	23; 0	30; 0
chr5:10401598@+	-300; 185	MARCH6	16; 0	23; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 18	1; 20
chr1:165624857@+	-127; 300	MGST3	11; 0	17; 0
chr19:17513754@-	-189; 300	BST2	8; 0	14; 0
chr17:57915758@+	-52; 300	TMEM49	10; 0	14; 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	10065	6.85%	20.82%	96.73%	7743	1.25655
anti	340	0.23%	0.70%	3.27%	289	0.0424469
both	10405	7.08%	21.52%	100.00%	8010	1.299
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	10693	6.65%	19.72%	96.80%	7743	1.33496
anti	353	0.22%	0.65%	3.20%	289	0.0440699
both	11046	6.87%	20.37%	100.00%	8010	1.37903

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	41; 0	65; 0
chr9:131456919@+	-292; 300	SET	31; 1	50; 1
chr2:211542610@+	-300; 300	CPS1	23; 0	33; 0
chr8:128753204@+	-241; 235	MYC	21; 0	31; 0
chr1:26227577@-	-160; 260	STMN1	20; 1	30; 1
chr10:112657785@+	-300; 300	PDCD4	20; 0	29; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	29; 0
chr2:189876353@+	-300; 210	COL3A1	17; 0	22; 0
chr4:24529663@-	-300; 283	DHX15	16; 0	24; 0
chr4:6643456@+	-236; 300	MRFAP1	16; 0	29; 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	41; 0	65; 0
chr9:131456919@+	-292; 300	SET	31; 1	50; 1
chr2:211542610@+	-300; 300	CPS1	23; 0	33; 0
chr8:128753204@+	-241; 235	MYC	21; 0	31; 0
chr1:26227577@-	-160; 260	STMN1	20; 1	30; 1
chr4:6643456@+	-236; 300	MRFAP1	16; 0	29; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	29; 0
chr10:112657785@+	-300; 300	PDCD4	20; 0	29; 0
chr4:24529663@-	-300; 283	DHX15	16; 0	24; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	22; 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	1110	0.76%	2.30%	46.46%	516	0.935919
anti	1279	0.87%	2.65%	53.54%	678	1.07841
both	2389	1.63%	4.94%	100.00%	1186	2.01433
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	1915	1.19%	3.53%	57.35%	516	1.61467
anti	1424	0.89%	2.63%	42.65%	678	1.20067
both	3339	2.08%	6.16%	100.00%	1186	2.81535

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	202; 0	374; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chrUn_gl000220:109077@+	-758; 300	18S	44; 0	61; 0
chr2:70315685@-	-1000; 62	AC136007.2	0; 32	0; 40
chr1:205685227@+	-1000; 300	AC119673.2	0; 26	0; 29
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 19	0; 22
chr17:57918626@+	-338; 36	hsa-mir-21	19; 0	28; 0
chr5:25190790@+	-1000; 176	RP11-184E9.1	0; 17	0; 22

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	202; 0	374; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	160; 0
chr14:74055600@-	-1000; 36	AC005225.1	5; 0	108; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	17; 0	96; 0
chrUn_gl000220:109077@+	-758; 300	18S	44; 0	61; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	14; 1	54; 1
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	13; 0	46; 0
chr7:96770956@-	-1000; 35	AC073421.1	6; 0	45; 0
chr2:70315685@-	-1000; 62	AC136007.2	0; 32	0; 40

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	1590	1.08%	3.29%	61.32%	755	1.21839
anti	1003	0.68%	2.07%	38.68%	563	0.768582
both	2593	1.76%	5.36%	100.00%	1305	1.98697
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	2307	1.44%	4.25%	67.87%	755	1.76782
anti	1092	0.68%	2.01%	32.13%	563	0.836782
both	3399	2.12%	6.27%	100.00%	1305	2.6046

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	274; 0	567; 0
chrUn_gl000220:110946@+	-300; 539	18S	30; 0	40; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 26	0; 36
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 21	0; 27
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 20	0; 25
chr2:191798136@-	-300; 1000	AC067945.1	0; 18	0; 18
chr1:17733878@+	-33; 1000	RP1-20B21.4	0; 17	0; 22
chr8:144939422@+	-300; 1000	AC105049.1	0; 16	0; 19
chr10:88810077@+	-38; 1000	AL136982.2	0; 16	0; 18

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	274; 0	567; 0
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr14:74055527@-	-37; 1000	AC005225.1	4; 0	56; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	10; 0	52; 0
chrUn_gl000220:110946@+	-300; 539	18S	30; 0	40; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 26	0; 36
chr3:14530617@-	-300; 1000	GRIP2	0; 21	0; 27
chr1:94312467@+	-40; 1000	hsa-mir-760	7; 0	27; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 20	0; 25
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	14; 0	23; 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	8167	5.56%	16.89%	98.50%	2659	2.99706
anti	124	0.08%	0.26%	1.50%	76	0.0455046
both	8291	5.64%	17.15%	100.00%	2725	3.04257
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	9538	5.94%	17.59%	98.62%	2659	3.50018
anti	133	0.08%	0.25%	1.38%	76	0.0488073
both	9671	6.02%	17.83%	100.00%	2725	3.54899

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	69; 0	119; 0
chr1:35650053@-	-70; 300	SFPQ	55; 0	78; 0
chr10:102120690@+	-100; 300	SCD	52; 0	89; 0
chr6:30692174@+	-300; 300	TUBB	38; 0	65; 0
chr3:149087560@-	-53; 300	TM4SF1	38; 0	56; 0
chr14:62213803@+	-76; 300	HIF1A	37; 0	55; 0
chr2:136872205@-	-300; 144	CXCR4	35; 0	43; 0
chrX:102931085@-	-300; 300	MORF4L2	34; 0	60; 0
chr9:33047287@-	-51; 300	SMU1	33; 0	47; 0
chr1:54497690@-	-144; 172	TMEM59	31; 0	40; 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	69; 0	119; 0
chr10:102120690@+	-100; 300	SCD	52; 0	89; 0
chr17:4849191@-	-50; 123	PFN1	26; 0	81; 0
chr1:35650053@-	-70; 300	SFPQ	55; 0	78; 0
chr6:30692174@+	-300; 300	TUBB	38; 0	65; 0
chrX:102931085@-	-300; 300	MORF4L2	34; 0	60; 0
chr3:149087560@-	-53; 300	TM4SF1	38; 0	56; 0
chr14:62213803@+	-76; 300	HIF1A	37; 0	55; 0
chr11:64532857@-	-66; 300	SF1	30; 0	52; 0
chr1:207533847@+	-300; 231	CD55	25; 0	50; 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	211	0.14%	0.44%	83.73%	146	1.30247
anti	41	0.03%	0.08%	16.27%	18	0.253086
both	252	0.17%	0.52%	100.00%	162	1.55556
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	224	0.14%	0.41%	83.27%	146	1.38272
anti	45	0.03%	0.08%	16.73%	18	0.277778
both	269	0.17%	0.50%	100.00%	162	1.66049

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; 19
chr6:31508971@-	-66; 265	BAT1	11; 0	16; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 8	0; 8
chr6:24718895@-	-300; 64	C6orf62	7; 0	9; 0
chr6:64286785@+	-92; 52	PTP4A1	7; 0	7; 0
chr8:101733810@-	-252; 96	PABPC1	5; 0	5; 0
chr19:49468764@+	-100; 51	FTL	5; 0	7; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	4; 0
chr17:43226557@+	-300; 300	HEXIM1	3; 1	3; 1
chr8:126011645@+	-300; 145	SQLE	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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 19
chr6:31508971@-	-66; 265	BAT1	11; 0	16; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	9; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 8	0; 8
chr6:64286785@+	-92; 52	PTP4A1	7; 0	7; 0
chr19:49468764@+	-100; 51	FTL	5; 0	7; 0
chr8:101733810@-	-252; 96	PABPC1	5; 0	5; 0
chr6:26271611@-	-216; 206	HIST1H3G	3; 0	4; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	4; 0
chr17:43226557@+	-300; 300	HEXIM1	3; 1	3; 1

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	177	0.12%	0.37%	27.15%	131	0.409722
anti	475	0.32%	0.98%	72.85%	311	1.09954
both	652	0.44%	1.35%	100.00%	432	1.50926
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	192	0.12%	0.35%	24.27%	131	0.444444
anti	599	0.37%	1.10%	75.73%	311	1.38657
both	791	0.49%	1.46%	100.00%	432	1.83102

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	20; 0	31; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 24
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 13	0; 14
chr20:47894962@-	-1000; 248	ZNFX1	0; 10	0; 10
chr5:175815975@-	-1000; 188	NOP16	0; 9	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr13:41635409@+	-1000; 200	WBP4	0; 8	0; 65
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 19
chr19:54960064@+	-920; 210	LENG8	0; 7	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)
chr13:41635409@+	-1000; 200	WBP4	0; 8	0; 65
chr15:89878025@-	-1000; 61	POLG	0; 7	0; 38
chr8:101734314@-	-1000; 252	PABPC1	20; 0	31; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 24
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 19
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 13	0; 14
chr5:175815975@-	-1000; 188	NOP16	0; 9	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr20:47894962@-	-1000; 248	ZNFX1	0; 10	0; 10

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	6791	4.62%	14.05%	85.56%	2574	2.31854
anti	1146	0.78%	2.37%	14.44%	434	0.39126
both	7937	5.40%	16.42%	100.00%	2929	2.7098
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	7646	4.76%	14.10%	84.90%	2574	2.61045
anti	1360	0.85%	2.51%	15.10%	434	0.464322
both	9006	5.60%	16.61%	100.00%	2929	3.07477

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; 49	0; 86
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 60
chr16:18802989@-	-300; 667	ARL6IP1	39; 0	53; 0
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr12:104744062@+	-300; 1000	TXNRD1	27; 0	39; 0
chr8:128753674@+	-235; 1000	MYC	26; 0	32; 0
chr15:45010359@+	-278; 1000	B2M	26; 0	32; 0
chrX:24096088@+	-282; 1000	EIF2S3	25; 0	29; 0
chr6:31785723@+	-132; 1000	HSPA1A	24; 0	32; 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)
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 60
chr16:18802989@-	-300; 667	ARL6IP1	39; 0	53; 0
chr2:1635657@-	-300; 1000	PXDN	19; 0	45; 0
chr12:104744062@+	-300; 1000	TXNRD1	27; 0	39; 0
chrX:70521018@+	-157; 282	NONO	14; 0	38; 0
chr17:79845715@-	-144; 1000	THOC4	19; 0	35; 0
chr8:128753674@+	-235; 1000	MYC	26; 0	32; 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	551	0.37%	1.14%	25.44%	324	0.464587
anti	1615	1.10%	3.34%	74.56%	879	1.36172
both	2166	1.47%	4.48%	100.00%	1186	1.82631
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	766	0.48%	1.41%	28.10%	324	0.645868
anti	1960	1.22%	3.61%	71.90%	879	1.65261
both	2726	1.70%	5.03%	100.00%	1186	2.29848

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	47; 1	54; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 44	0; 117
chrUn_gl000220:109077@+	-758; 300	18S	44; 0	61; 0
chr2:70315685@-	-1000; 62	AC136007.2	0; 32	0; 40
chr1:205685227@+	-1000; 300	AC119673.2	0; 26	0; 29
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr8:101734314@-	-1000; 252	PABPC1	20; 0	31; 0
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 19	0; 22
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19

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	17; 0	160; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 44	0; 117
chr13:41635409@+	-1000; 200	WBP4	0; 8	0; 65
chrUn_gl000220:109077@+	-758; 300	18S	44; 0	61; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chr2:70315685@-	-1000; 62	AC136007.2	0; 32	0; 40
chr15:89878025@-	-1000; 61	POLG	0; 7	0; 38
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chrM:5903@+	-162; 300	J01415.8	0; 5	0; 32
chr8:101734314@-	-1000; 252	PABPC1	20; 0	31; 0

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	8304	5.65%	17.18%	80.74%	3133	2.15018
anti	1981	1.35%	4.10%	19.26%	826	0.512947
both	10285	7.00%	21.28%	100.00%	3862	2.66313
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	9843	6.12%	18.15%	80.98%	3133	2.54868
anti	2312	1.44%	4.26%	19.02%	826	0.598654
both	12155	7.56%	22.41%	100.00%	3862	3.14733

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	274; 0	567; 0
chr1:169101767@-	-127; 1000	NME7	1; 64	1; 91
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 60
chr7:5566780@-	-300; 1000	ACTB	43; 0	109; 0
chr16:18802989@-	-300; 667	ARL6IP1	39; 0	53; 0
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chrUn_gl000220:110946@+	-300; 539	18S	30; 0	40; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr12:104744062@+	-300; 1000	TXNRD1	27; 0	39; 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	274; 0	567; 0
chr7:5566780@-	-300; 1000	ACTB	43; 0	109; 0
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr1:169101767@-	-127; 1000	NME7	1; 64	1; 91
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr6:26031876@-	-206; 1000	HIST1H3B	15; 0	85; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr1:153516087@-	-156; 923	S100A4	18; 0	68; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 60

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	5386	3.66%	11.14%	96.21%	4596	1.13056
anti	212	0.14%	0.44%	3.79%	173	0.0445004
both	5598	3.81%	11.58%	100.00%	4764	1.17506
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	5606	3.49%	10.34%	96.24%	4596	1.17674
anti	219	0.14%	0.40%	3.76%	173	0.0459698
both	5825	3.62%	10.74%	100.00%	4764	1.22271

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)
chr9:86584384@-	-300; 90	HNRNPK	10; 0	24; 0
chr6:31508624@-	-300; 100	BAT1	10; 0	13; 0
chr5:10401919@+	-300; 100	MARCH6	10; 0	13; 0
chr20:34326966@-	-300; 28	RBM39	10; 0	10; 0
chr1:1326494@-	-300; 100	CCNL2	10; 0	10; 0
chr5:179048854@-	-300; 100	HNRNPH1	9; 0	9; 0
chr16:31199583@+	-300; 60	FUS	9; 0	10; 0
chr7:148514576@-	-149; 94	EZH2	7; 0	8; 0
chr6:144286222@-	-300; 100	PLAGL1	6; 0	7; 0
chr5:179045370@-	-300; 47	HNRNPH1	6; 0	10; 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	24; 0
chr6:31508624@-	-300; 100	BAT1	10; 0	13; 0
chr5:10401919@+	-300; 100	MARCH6	10; 0	13; 0
chr5:179045370@-	-300; 47	HNRNPH1	6; 0	10; 0
chr20:34326966@-	-300; 28	RBM39	10; 0	10; 0
chr16:31199583@+	-300; 60	FUS	9; 0	10; 0
chr1:1326494@-	-300; 100	CCNL2	10; 0	10; 0
chr1:28835317@+	-300; 22	SNHG3	5; 0	10; 0
chr5:179048854@-	-300; 100	HNRNPH1	9; 0	9; 0
chr7:148514576@-	-149; 94	EZH2	7; 0	8; 0

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