Parameters
input_file: 20091102_LUjt5_8_hg19_ensembl59_S_iCLIP_TDP-43_SHSY5Y_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: 170608
[x-link sites] used in any map: 25244 (14.80%)
[single hits (=G+T), cDNA counts] total: 170608
[single hits (=G+T), cDNA counts] used in any map: 31389 (16.46%)

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	7452	4.37%	29.52%	8116	4.26%	25.86%
intron-exon	-300; 300	7056	4.14%	27.95%	7709	4.04%	24.56%
5-ncRNA	-1000; 300	2219	1.30%	8.79%	3964	2.08%	12.63%
ncRNA-3	-300; 1000	2492	1.46%	9.87%	5002	2.62%	15.94%
ORF-3UTR	-300; 300	1074	0.63%	4.25%	1173	0.62%	3.74%
5UTR-ORF	-300; 300	157	0.09%	0.62%	202	0.11%	0.64%
inter-5UTR	-1000; 300	581	0.34%	2.30%	734	0.38%	2.34%
3UTR-inter	-300; 1000	1858	1.09%	7.36%	2011	1.05%	6.41%
inter-5	-1000; 300	1805	1.06%	7.15%	3212	1.68%	10.23%
3-inter	-300; 1000	3343	1.96%	13.24%	5522	2.90%	17.59%
BP best in intron	-300; 100	5775	3.38%	22.88%	6309	3.31%	20.10%

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	6987	4.10%	27.68%	93.76%	5120	1.2699
anti	465	0.27%	1.84%	6.24%	396	0.0845147
both	7452	4.37%	29.52%	100.00%	5502	1.35442
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	7579	3.97%	24.15%	93.38%	5120	1.3775
anti	537	0.28%	1.71%	6.62%	396	0.0976009
both	8116	4.26%	25.86%	100.00%	5502	1.4751

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)
chr11:12886447@+	-32; 300	TEAD1	21; 0	25; 0
chr15:37391100@-	-248; 299	MEIS2	19; 0	29; 0
chr3:128206552@-	-106; 300	GATA2	18; 0	23; 0
chr2:242608275@+	-300; 300	ATG4B	17; 0	21; 0
chr1:156845458@+	-74; 206	NTRK1	17; 0	24; 0
chr3:50407749@-	-31; 300	CACNA2D2	16; 0	17; 0
chr1:1158622@-	-57; 300	SDF4	15; 0	18; 0
chr7:128001358@-	-190; 300	PRRT4	14; 0	17; 0
chr17:38506177@+	-71; 300	RARA	14; 0	14; 0
chr1:50575636@+	-75; 300	ELAVL4	14; 0	15; 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	54; 0
chr15:37391100@-	-248; 299	MEIS2	19; 0	29; 0
chr11:12886447@+	-32; 300	TEAD1	21; 0	25; 0
chr1:156845458@+	-74; 206	NTRK1	17; 0	24; 0
chr3:128206552@-	-106; 300	GATA2	18; 0	23; 0
chr2:242608275@+	-300; 300	ATG4B	17; 0	21; 0
chr22:50661414@-	-300; 197	TUBGCP6	12; 0	18; 0
chr1:1158622@-	-57; 300	SDF4	15; 0	18; 0
chr7:128001358@-	-190; 300	PRRT4	14; 0	17; 0
chr3:50407749@-	-31; 300	CACNA2D2	16; 0	17; 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	6653	3.90%	26.35%	94.29%	5098	1.2241
anti	403	0.24%	1.60%	5.71%	351	0.074149
both	7056	4.14%	27.95%	100.00%	5435	1.29825
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	7185	3.77%	22.89%	93.20%	5098	1.32199
anti	524	0.27%	1.67%	6.80%	351	0.0964121
both	7709	4.04%	24.56%	100.00%	5435	1.4184

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)
chr10:43604478@+	-300; 100	RET	40; 0	78; 0
chr3:64502796@-	-300; 300	ADAMTS9	27; 0	38; 0
chr10:43595906@+	-300; 132	RET	25; 0	30; 0
chr15:37388630@-	-300; 71	MEIS2	17; 0	22; 0
chr8:11640711@+	-300; 98	NEIL2	16; 0	18; 0
chr20:60912041@-	-300; 41	LAMA5	16; 0	22; 0
chr15:75308933@+	-300; 78	SCAMP5	15; 0	16; 0
chr20:62364570@+	-300; 67	ZGPAT	13; 0	13; 0
chr12:124915332@-	-300; 86	NCOR2	13; 0	14; 0
chr1:156834145@+	-300; 37	NTRK1	13; 0	13; 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)
chr10:43604478@+	-300; 100	RET	40; 0	78; 0
chr1:162330326@+	-300; 194	NOS1AP	0; 5	0; 42
chr3:64502796@-	-300; 300	ADAMTS9	27; 0	38; 0
chr10:43595906@+	-300; 132	RET	25; 0	30; 0
chr5:3600722@+	-174; 36	IRX1	0; 6	0; 29
chrX:107408267@-	-166; 81	COL4A6	0; 4	0; 26
chr20:60912041@-	-300; 41	LAMA5	16; 0	22; 0
chr15:37388630@-	-300; 71	MEIS2	17; 0	22; 0
chr8:11640711@+	-300; 98	NEIL2	16; 0	18; 0
chrX:118754013@-	-300; 300	SEPT6	12; 0	16; 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	1233	0.72%	4.88%	55.57%	572	1.01148
anti	986	0.58%	3.91%	44.43%	659	0.80886
both	2219	1.30%	8.79%	100.00%	1219	1.82034
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	2886	1.51%	9.19%	72.81%	572	2.36751
anti	1078	0.57%	3.43%	27.19%	659	0.884331
both	3964	2.08%	12.63%	100.00%	1219	3.25185

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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	79; 0	268; 0
chr11:65269806@+	-1000; 29	MALAT1	67; 0	89; 0
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	33; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr22:50295450@+	-1000; 30	AL671710.1	13; 1	13; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	13; 0	70; 0
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 12	0; 12

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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	79; 0	268; 0
chrM:5890@-	-777; 32	J01415.32	5; 4	99; 5
chr11:65269806@+	-1000; 29	MALAT1	67; 0	89; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	13; 0	70; 0
chr17:38273625@-	-1000; 37	AC068669.1	2; 0	49; 0
chr14:74055600@-	-1000; 36	AC005225.1	6; 0	40; 0
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	33; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr17:62223442@+	-1000; 35	SNORND104	11; 0	24; 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	1472	0.86%	5.83%	59.07%	615	1.18519
anti	1020	0.60%	4.04%	40.93%	639	0.821256
both	2492	1.46%	9.87%	100.00%	1242	2.00644
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	3836	2.01%	12.22%	76.69%	615	3.08857
anti	1166	0.61%	3.71%	23.31%	639	0.938808
both	5002	2.62%	15.94%	100.00%	1242	4.02738

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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	46; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	54; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:19153894@+	-300; 1000	AC003986.6	0; 16	0; 17
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	14; 0	30; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	189; 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	414; 0	2219; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	189; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	54; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	46; 0
chr17:38273551@-	-37; 1000	AC068669.1	2; 0	46; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chr3:186504641@+	-89; 137	EIF4A2, SNORA81-ENSG00000221420	13; 0	35; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	14; 0	30; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 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	982	0.58%	3.89%	91.43%	606	1.43988
anti	92	0.05%	0.36%	8.57%	77	0.134897
both	1074	0.63%	4.25%	100.00%	682	1.57478
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	1076	0.56%	3.43%	91.73%	606	1.57771
anti	97	0.05%	0.31%	8.27%	77	0.142229
both	1173	0.62%	3.74%	100.00%	682	1.71994

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)
chr7:92244026@-	-287; 300	CDK6	28; 0	38; 0
chr16:29831075@+	-100; 300	C16orf53	27; 0	29; 0
chr7:100806072@-	-56; 142	VGF	16; 0	37; 0
chr17:45016126@+	-81; 300	GOSR2	13; 0	14; 0
chr1:11083386@+	-69; 300	TARDBP	12; 0	13; 0
chr7:26252043@+	-171; 300	CBX3	11; 0	12; 0
chr4:174448424@-	-51; 300	HAND2	10; 0	11; 0
chr10:94837061@+	-171; 293	CYP26A1	8; 0	8; 0
chr22:19025348@-	-300; 300	DGCR2	7; 0	7; 0
chr6:7289914@-	-84; 300	SSR1	6; 0	7; 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)
chr7:92244026@-	-287; 300	CDK6	28; 0	38; 0
chr7:100806072@-	-56; 142	VGF	16; 0	37; 0
chr16:29831075@+	-100; 300	C16orf53	27; 0	29; 0
chr17:45016126@+	-81; 300	GOSR2	13; 0	14; 0
chr1:11083386@+	-69; 300	TARDBP	12; 0	13; 0
chr7:26252043@+	-171; 300	CBX3	11; 0	12; 0
chr4:71655313@+	-51; 243	RUFY3	6; 0	12; 0
chr4:174448424@-	-51; 300	HAND2	10; 0	11; 0
chr16:67472427@-	-82; 253	ATP6V0D1	6; 0	8; 0
chr10:94837061@+	-171; 293	CYP26A1	8; 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.

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	134	0.08%	0.53%	85.35%	85	1.31373
anti	23	0.01%	0.09%	14.65%	17	0.22549
both	157	0.09%	0.62%	100.00%	102	1.53922
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	145	0.08%	0.46%	71.78%	85	1.42157
anti	57	0.03%	0.18%	28.22%	17	0.558824
both	202	0.11%	0.64%	100.00%	102	1.98039

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)
chr2:61764828@-	-277; 66	XPO1	10; 0	11; 0
chr6:31508971@-	-66; 265	BAT1	9; 0	13; 0
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chr16:89980628@+	-52; 300	AC092143.1	6; 0	6; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr17:47755471@-	-62; 89	SPOP	5; 0	7; 0
chr1:50575487@+	-95; 74	ELAVL4	4; 0	4; 0
chr7:69064639@+	-300; 154	AUTS2	3; 0	3; 0
chr6:7542148@+	-171; 85	DSP	0; 3	0; 37
chr5:86564268@+	-282; 269	RASA1	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)
chr6:7542148@+	-171; 85	DSP	0; 3	0; 37
chr6:31508971@-	-66; 265	BAT1	9; 0	13; 0
chr2:61764828@-	-277; 66	XPO1	10; 0	11; 0
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chr17:47755471@-	-62; 89	SPOP	5; 0	7; 0
chr16:89980628@+	-52; 300	AC092143.1	6; 0	6; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr1:50575487@+	-95; 74	ELAVL4	4; 0	4; 0
chr7:69064639@+	-300; 154	AUTS2	3; 0	3; 0
chr5:86564268@+	-282; 269	RASA1	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-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	221	0.13%	0.88%	38.04%	144	0.626062
anti	360	0.21%	1.43%	61.96%	213	1.01983
both	581	0.34%	2.30%	100.00%	353	1.64589
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	254	0.13%	0.81%	34.60%	144	0.719547
anti	480	0.25%	1.53%	65.40%	213	1.35977
both	734	0.38%	2.34%	100.00%	353	2.07932

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)
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 0
chr2:72375166@-	-1000; 88	CYP26B1	11; 0	13; 0
chr1:151030233@+	-1000; 300	MLLT11	0; 11	0; 14
chr21:38445469@-	-1000; 90	PIGP	0; 10	0; 10
chr11:62623517@+	-1000; 112	SLC3A2	0; 9	0; 10
chr16:89980524@+	-1000; 52	AC092143.1	8; 0	8; 0
chr6:127664753@-	-1000; 137	ECHDC1	0; 7	0; 7
chr5:36152062@-	-1000; 203	LMBRD2	0; 7	0; 8

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)
chr15:89878025@-	-1000; 61	POLG	0; 6	0; 48
chr13:41635409@+	-1000; 200	WBP4	0; 4	0; 25
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr19:49955066@-	-1000; 118	PIH1D1	2; 0	19; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 5	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr1:151030233@+	-1000; 300	MLLT11	0; 11	0; 14
chr2:72375166@-	-1000; 88	CYP26B1	11; 0	13; 0
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 0
chr17:37026255@+	-1000; 93	LASP1	0; 2	0; 11

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	1500	0.88%	5.94%	80.73%	924	1.29199
anti	358	0.21%	1.42%	19.27%	247	0.308355
both	1858	1.09%	7.36%	100.00%	1161	1.60034
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	1631	0.86%	5.20%	81.10%	924	1.40482
anti	380	0.20%	1.21%	18.90%	247	0.327304
both	2011	1.05%	6.41%	100.00%	1161	1.73213

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)
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chr2:69686412@-	-300; 1000	AC114772.2	13; 0	15; 0
chr10:43625799@+	-300; 1000	RET	12; 0	12; 0
chr1:179785333@+	-300; 1000	FAM163A	12; 0	13; 0
chr7:47314750@-	-300; 1000	TNS3	11; 0	11; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	18; 0
chr3:115528639@-	-241; 1000	LSAMP	10; 0	11; 0
chr19:47278138@-	-300; 1000	SLC1A5	10; 0	10; 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)
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chr7:100805788@-	-142; 1000	VGF	10; 0	18; 0
chr19:18390561@-	-300; 1000	JUND	8; 0	18; 0
chr2:69686412@-	-300; 1000	AC114772.2	13; 0	15; 0
chr1:180859387@+	-300; 1000	XPR1	10; 0	14; 0
chr1:179785333@+	-300; 1000	FAM163A	12; 0	13; 0
chr7:102740021@-	-100; 1000	NAPEPLD	0; 9	0; 12
chr10:102309763@+	-300; 1000	HIF1AN	10; 0	12; 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	627	0.37%	2.48%	34.74%	341	0.586529
anti	1178	0.69%	4.67%	65.26%	738	1.10196
both	1805	1.06%	7.15%	100.00%	1069	1.68849
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	1749	0.92%	5.57%	54.45%	341	1.63611
anti	1463	0.77%	4.66%	45.55%	738	1.36857
both	3212	1.68%	10.23%	100.00%	1069	3.00468

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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 30	0; 50
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	33; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 12	0; 12
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chrM:5903@+	-162; 300	J01415.8	1; 7	1; 101
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 30	0; 50
chr15:89878025@-	-1000; 61	POLG	0; 6	0; 48
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	33; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr13:41635409@+	-1000; 200	WBP4	0; 4	0; 25
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20

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	2309	1.35%	9.15%	69.07%	1160	1.28635
anti	1034	0.61%	4.10%	30.93%	650	0.576045
both	3343	1.96%	13.24%	100.00%	1795	1.8624
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	4370	2.29%	13.92%	79.14%	1160	2.43454
anti	1152	0.60%	3.67%	20.86%	650	0.641783
both	5522	2.90%	17.59%	100.00%	1795	3.07632

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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	46; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:19153894@+	-300; 1000	AC003986.6	0; 16	0; 17
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39

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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	46; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr20:32500127@-	-217; 1000	TPM5P	3; 0	22; 0
chr2:158155317@-	-176; 1000	7SK-ENSG00000222404	0; 3	0; 22

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	5481	3.21%	21.71%	94.91%	3995	1.28904
anti	294	0.17%	1.16%	5.09%	267	0.0691439
both	5775	3.38%	22.88%	100.00%	4252	1.35818
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	5963	3.13%	19.00%	94.52%	3995	1.4024
anti	346	0.18%	1.10%	5.48%	267	0.0813735
both	6309	3.31%	20.10%	100.00%	4252	1.48377

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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	36; 0	68; 0
chr10:43595881@+	-300; 23	RET	25; 0	30; 0
chr15:37388702@-	-300; 95	MEIS2	19; 0	24; 0
chr20:62364539@+	-300; 29	ZGPAT	16; 0	16; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	16; 0
chr12:124915763@-	-300; 100	NCOR2	15; 0	16; 0
chr1:156834120@+	-300; 23	NTRK1	15; 0	15; 0
chr20:32661328@+	-300; 38	RALY	14; 0	16; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	39; 0
chr15:37390646@-	-300; 100	MEIS2	13; 0	19; 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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	36; 0	68; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	39; 0
chr10:43595881@+	-300; 23	RET	25; 0	30; 0
chrX:107408303@-	-130; 36	COL4A6	0; 4	0; 26
chr15:37388702@-	-300; 95	MEIS2	19; 0	24; 0
chr15:37390646@-	-300; 100	MEIS2	13; 0	19; 0
chrX:118754079@-	-300; 66	SEPT6	12; 0	16; 0
chr20:62364539@+	-300; 29	ZGPAT	16; 0	16; 0
chr20:32661328@+	-300; 38	RALY	14; 0	16; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	16; 0

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