GapOverlap

methods

The measurements are taken from the gapOverlap.bed[.gz] file in /hive/data/genomes/<db>/bed/gapOverlap/gapOverlap.bed[.gz] The score column in the bed file (column 5) is the size of the duplicated sequence. The gap size between the duplicated sequence is calculated from: end - start + 2 * score

The item total is the sum of the sizes of the duplicated sequences. Not both sides though, just one side. This indicates how much sequence is duplicated.

The gap total is the sum of the sizes of all the gaps involved.

table features

The table columns can be sorted, click on the up/down arrow icon in the column header. The 'year' is what we have in the dbDb table as indicated from the assembly information files for the date of the assembly. A few do not have dates (set to 1880), and do not have database genome browsers

These ends were found by taking 1,000 bases on each side of any run of N's in the sequence, thus any gap, and aligned with the blat command:

 blat -q=dna -minIdentity=95 -repMatch=10 upstream.fa downstream.fa

Filtering the PSL output for a perfect match, no mis-matches, and therefore of equal size matching sequence, where the alignment ends exactly at the end of the upstream sequence before the gap and begins exactly at the start of the downstream sequence after the gap.

gapOverlap table statistics

count	year	dbName	item count	item median	item total	gap median	gap total
001	2013	CHM1	85	86	10897	88	65164
002	2014	acaChl1	5	17	1250	188	2340
005	2009	ailMel1	48	104	10594	1193	82504
006	2012	allMis1	1151	83	273934	1	74939
007	2013	allSin1	95	125	26114	2265	261774
008	2013	amaVit1	10099	81	1392334	172	2756641
009	2013	anaPla1	31	251	10663	166	94318
010	2014	ancCey1	805	154	171926	1	85569
011	2014	angJap1	4539	91	477038	1	610535
012	2007	anoCar1	20	383.5	8167	537.5	23338
013	2010	anoCar2	25	24	6694	258	26105
014	2003	anoGam1	7	528	3139	1	21041
015	2013	apaSpi1	607	61	34340	1	56961
017	2004	apiMel1	216	5	12150	1	24454
018	2005	apiMel2	133	5	7371	5	19757
019	2005	apiMel3	199	62	16045	5	27354
020	2010	apiMel4	226	52.5	13378	5	24561
021	2008	aplCal1	25	77	3383	1	16863
022	2014	aptFor1	109	147	26798	1575	323838
023	2015	aptMan1	15742	124	4653010	1	3331011
024	2014	aquChr1	4592	43	201248	65	16118238
025	2014	aquChr2	326	82.5	31349	1	143600
026	2013	araMac1	120	48.5	7929	33	27135
027	1880	araTha1	1	289	289	6	60
028	2012	ascSuu1	9	404	3688	555	6481
029	2013	astMex1	1385	78	137888	1	1964877
030	2013	balAcu1	211	149	57860	821	371511
031	2014	balPav1	5	27	1303	216	1098
032	2014	bisBis1	8184	72	712109	1	947641
034	2011	bosMut1	139	83	27917	1274	256420
035	2004	bosTau1	6550	4	289123	5	609155
036	2005	bosTau2	4361	105	564259	5	2525381
037	2006	bosTau3	411	51	38673	5	270212
038	2007	bosTau4	437	53	52814	5	376407
039	2009	bosTau5	435	53	51742	5	376650
040	2009	bosTau6	789	67	463109	1	87080
041	2011	bosTau7	413	55	39706	5	141131
042	2014	bosTau8	789	67	463109	1	87080
043	2009	bosTauMd3	789	67	463109	1	87080
044	2006	braFlo1	31	484	14260	417	12668
045	2008	braFlo2	22	439	8529	411	9064
046	1880	braRap1	12	104	3193	281	47557
047	2007	bruMal1	55	5	6093	1	18780
048	2014	bruMal2	46	124.5	12221	431.5	63506
049	2013	bubBub1	2383	163	395268	1	251657
050	2014	bucRhi1	31	114	5089	78	3263
052	2011	burXyl1	65	601	33110	301	19553
053	2010	caeAng1	414	41	16726	2	1802
054	2012	caeAng2	461	46	19505	2	1495
055	2008	caeJap1	135	58	10431	186	27893
056	2009	caeJap2	765	103	130030	1018	891958
057	1880	caeJap2a	764	103	129273	1018	890958
059	2010	caeJap4	16	98.5	3188	2	1468
060	2007	caePb1	115	44	9160	164	37674
061	2008	caePb2	83	37	3814	222	63681
062	2010	caePb3	89	37	4915	222	74680
063	2005	caeRem1	58	96	10213	133.5	11238
064	2006	caeRem2	58	96	10213	133.5	11238
065	2007	caeRem3	46	5	5760	197.5	14178
066	2007	caeRem4	46	5	5760	197.5	14178
067	2010	caeSp111	4	194.5	760	2	80
068	2012	caeSp51	14	34	730	12.5	894
069	2010	caeSp71	535	47	30250	213	312209
070	2010	caeSp91	26	217.5	7172	8745	180575
071	2014	calAnn1	89	127	16337	1006	168943
072	2007	calJac1	1597	42	129367	182	377725
073	2009	calJac3	1516	43	116646	183.5	452860
074	2013	calMil1	31	123	8335	1	70257
075	2011	camFer1	11	205	2059	129	2031
076	2004	canFam1	12	153	2669	210.5	8118
077	2005	canFam2	32	199.5	8095	1	5245
078	2011	canFam3	34	175.5	8234	1	4545
081	2014	capCar1	4	105	618	48	354
082	2012	capHir1	627	41	71810	1	546475
083	2014	carCri1	4	161	644	210.5	878
084	2005	cavPor2	393	427	164744	1	166667
085	2008	cavPor3	3	145	552	1	961
086	2002	cb1	81	163	20408	145	39126
087	2005	cb2	86	153	21033	163.5	42461
088	2007	cb3	80	148.5	19176	166.5	39580
089	2011	cb4	86	153	20969	151.5	40114
100	2012	cerSim1	1818	68	129697	1	270005
101	2014	chaVoc1	47	2	13700	1514	133699
102	2014	chaVoc2	47	2	13700	1514	133699
103	2013	cheMyd1	129	204	37111	798	277853
104	2012	chiLan1	1183	7	101029	1	267937
105	2013	chlSab1	23634	81	2123928	1	396229
106	2014	chlSab2	23631	81	2123656	1	396199
107	2014	chlUnd1	5	293	1223	129	617
108	2008	choHof1	104	54.5	14520	145.5	33892
109	2012	chrAsi1	3416	76	339291	1	720504
110	2011	chrPic1	7555	79	738667	5	1230115
111	2014	chrPic2	6315	77	629230	206	2593694
112	2002	ci1	28	311.5	8955	5	11060
113	2005	ci2	2	472.5	945	173	346
114	2011	ci3	22	258.5	6455	5	9493
115	2003	cioSav1	8	124	1554	1	2755
116	2005	cioSav2	6	402.5	2394	2	1668
117	2015	colAng1	5690	77	626146	5	1472786
118	2013	colLiv1	19	116	3824	129	32865
119	2014	colStr1	5	161	910	308	1203
120	2012	conCri1	1110	72	108033	1	233431
121	2014	corBra1	41	9	7520	1445	112176
122	2014	corCor1	21	81	2189	1027	27602
123	2013	cotJap1	1122	33	38101	68	67651
124	2013	criGri1	588	217	196516	1481.5	1359815
125	2011	criGriChoV1	213	162	53736	1526	472877
126	2014	cucCan1	113	242	41656	972	203191
127	2014	cynSem1	78	311.5	27891	935.5	165198
128	2014	cypVar1	3240	89	423504	1	2210432
129	2003	danRer1	1280	57	186413	1	322061
130	2014	danRer10	575	174	105525	1	17550
131	2004	danRer2	1150	58	191859	1	223764
132	2005	danRer3	819	58	88143	1	121196
133	2006	danRer4	726	65.5	121967	14	135012
134	2007	danRer5	1559	17	288298	1	155702
135	2008	danRer6	1421	133	225674	1	142101
136	2010	danRer7	1245	164	217595	1	124500
137	2005	dasNov1	55	123	12971	111	31368
138	2008	dasNov2	109	136	25865	1	58752
139	2011	dasNov3	239	46	16270	5	94236
140	2014	dicLab1	275	423	116519	203	134149
141	2008	dipOrd1	219	46	46012	379	102683
142	2013	dirImm1	505	175	132528	2	32073
143	2003	dm1	9	252	2984	2	1237
144	2004	dm2	8	362	2818	2	1217
145	2006	dm3	20	286	4907	1	423940
146	2014	dm6	15	333	4828	1	1340
147	2003	dp2	113	64	11633	1	9049
148	2004	dp3	136	79.5	17354	79.5	14988
149	2006	dp4	183	81	19720	5	18528
150	2012	droAlb1	4360	3	131320	22	152454
151	2004	droAna1	103	252	28853	1	10300
152	2005	droAna2	32	16	7905	701	72786
153	2006	droAna3	35	143	8663	671	75001
154	2013	droBia2	14	116.5	2103	2	294
155	2013	droBip2	26	103.5	3925	2	520
156	2013	droEle2	22	205	4879	2	440
157	2005	droEre1	8	86.5	1545	731	6855
158	2006	droEre2	14	221	4384	239	7433
159	2013	droEug2	17	52	1627	2	237
160	2013	droFic2	11	352	3277	2	220
161	2005	droGri1	17	76	2908	444	11143
162	2006	droGri2	48	60.5	5904	430.5	52107
163	2013	droKik2	12	102	1812	2	1721
164	2013	droMir2	122	72	16465	1	57520
166	2005	droMoj2	22	219.5	7748	366.5	30847
167	2006	droMoj3	16	343	6118	426	29359
168	2005	droPer1	28	402	10502	1	10914
169	2013	droPse3	12	51	1309	86	3307
170	2013	droRho2	35	167	7228	2	1286
171	2005	droSec1	17	399	6822	1	5318
172	2005	droSim1	109	106	23001	298	40703
173	2014	droSim2	104	58	5999	1	1818
174	2013	droSuz1	71	185	16489	1565	196054
175	2013	droTak2	13	102	2070	2	260
176	2004	droVir1	48	328.5	15839	25	16648
177	2005	droVir2	13	232	3421	1415	46365
178	2006	droVir3	12	341	4206	1536.5	45200
179	2006	droWil1	23	248	8712	133	51159
180	2006	droWil2	23	248	8712	133	51159
181	2004	droYak1	65	34	25549	25	24358
182	2005	droYak2	99	17	26922	54	37713
183	2006	droYak3	85	143	20479	1	23713
187	2005	echTel1	89	83	17114	1	22024
188	2012	echTel2	3871	93	620444	1	656358
189	2014	egrGar1	112	213.5	33121	1093.5	229589
190	2013	eidHel1	27	45	1294	1	186
191	2012	eleEdw1	1643	71	141553	1	311199
192	2012	eptFus1	1641	75	188916	1	378407
193	2007	equCab1	17	457	5982	1	6200
194	2007	equCab2	4	160.5	610	1909	18507
195	2014	equPrz1	39	49	5163	49	12408
196	2006	eriEur1	343	435	146738	1	209198
197	2012	eriEur2	3596	7	265454	1	1205265
198	2014	esoLuc1	9785	81	734131	15	1227519
200	2014	eurHel1	2	89.5	179	436	872
202	2013	falChe1	27	206	7614	685	35918
203	2013	falPer1	6	48.5	530	631.5	4836
204	1880	felCat1	1343	353	504058	874	2708782
205	2006	felCat3	1343	353	504058	874	2708782
206	2008	felCat4	9736	503	4582767	1	9398414
207	2011	felCat5	27	72	6437	2	100569
208	2014	felCat8	630	55	50300	1	89447
209	2013	ficAlb2	632	77	75592	40.5	206854
210	2002	fr1	76	155.5	19306	5	16684
211	2004	fr2	5	313	1682	512	2231
212	2011	fr3	6	229	1827	286	2291
213	2014	fulGla1	8	336.5	2583	103.5	1637
214	2010	gadMor1	168	53	11363	27	70748
215	2004	galGal2	114	4	12930	124	17674
216	2006	galGal3	729	37	34199	5	325853
217	2011	galGal4	55	401	22946	1	31537
218	2015	galGal5	1	33	33	795	795
219	2014	galVar1	58964	61	5626241	419	24866346
220	2006	gasAcu1	8	46.5	1970	117.5	2520
222	2009	gavGan0	30236	134	5187944	5	145799649
223	2014	gavSte1	5	164	848	318	2312
224	2012	geoFor1	32	105.5	4877	945.5	51025
226	2009	gorGor2	6585	247	2365617	1	499615
227	2011	gorGor3	6926	246	2475426	1	533805
228	2014	gorGor4	8691	94	1514940	25	982883
230	2009	haeCon1	25	39	1031	1	1745
231	2013	haeCon2	5378	149	831727	55	351011
232	2014	halAlb1	11	126	1936	37	3807
233	2014	halLeu1	14	28	4342	95	1676
234	2011	hapBur1	965	95	135908	2	374038
235	2011	hetBac1	3	228	1282	2	60
236	2011	hetGla1	743	313	285174	1994	2914751
237	2012	hetGla2	595	7	44604	1	201552
238	2009	hg19	1	2	200	3	3000000
243	2013	hg38	12	78	974	44	56689
252	2012	jacJac1	2666	63	196366	1	569918
253	2011	latCha1	2038	77	159059	1	504858
255	2014	lepDis1	1	5	50	229	229
256	2011	lepOcu1	2079	95	232474	1	466733
257	2013	lepWed1	2022	63	135843	1	1218867
258	2013	letCam1	1453	69	123952	1	739039
259	1880	linHum0	179	48	10176	1	20986
260	2013	lipVex1	292	92	66483	985.5	386576
261	2012	loaLoa1	376	382	123384	215	94547
262	2005	loxAfr1	79	44	11426	206	80801
263	2008	loxAfr2	78	165.5	20735	1078	180887
264	2009	loxAfr3	11	45	1924	398	9784
265	2007	macEug1	7319	57	504656	1	562759
266	2009	macEug2	11689	55	752361	5	1102638
267	2013	macFas5	1138	106.5	145024	204.5	1039415
268	2015	macNem1	1828	95	237662	5	834836
269	2014	manPen1	37129	101	5536376	1	13090743
270	2014	manVit1	25	231	8844	1303	65245
272	2012	mayZeb1	1831	95	241336	1	682313
273	2013	megLyr1	33	38	1716	1	185
274	2009	melGal1	834	127	136229	1	661041
275	2014	melGal5	84	181	17431	1	76065
278	2008	melInc2	3	77	211	201	513
279	2011	melUnd1	39	89	5925	41	36796
280	2014	merNub1	2	154.5	309	361	722
281	2013	mesAur1	3589	71	248381	1	755166
282	2014	mesUni1	4	347	1434	124.5	451
283	1880	micMur0	295	256	90483	78	749299
284	2007	micMur1	124	124.5	33320	952.5	207469
285	2015	micMur2	774	9	85250	5	267164
286	2017	micMur3	325	95	73918	5	262987
287	2012	micOch1	6788	65	483435	1	1507707
288	2011	mm10	2	390.5	781	25879.5	51759
292	1880	mm5	204	48.5	30180	1	76884
293	2005	mm6	117	48	17647	1	48212
294	2005	mm7	45	48	5475	1	64491
295	2006	mm8	6	161	1257	162.5	50878
296	2007	mm9	2	390.5	781	25879.5	51759
297	2004	monDom1	18	53.5	1891	127	11341
298	2005	monDom2	5	428	2012	1	520
299	2006	monDom4	9	183	3070	1	21732
300	2006	monDom5	9	183	3070	1	21732
301	2013	musDom2	1284	85	165577	1	473996
302	2011	musFur1	1009	84	107706	44	286510
303	2013	myoBra1	356	119	85889	1109	766318
304	2012	myoDav1	303	151	56967	1283	942238
305	2006	myoLuc1	42	47	6392	1551	125787
306	2010	myoLuc2	7	39	357	41	3363
307	2014	nanGal1	730	126	149781	902.5	980462
308	2015	nanPar1	1716	194	477991	974	2590489
309	2014	nasLar1	614	43	93736	7	126885
310	2013	necAme1	459	54	28538	1	92887
311	2007	nemVec1	25	378	10288	829	17106
312	2011	neoBri1	5040	95	1321574	2	665865
313	2014	nipNip1	41	154	11937	109	77358
314	2010	nomLeu1	859	141	220161	532	1139352
315	2011	nomLeu2	859	141	220161	532	1139352
316	2012	nomLeu3	861	141	220464	519	1139552
317	2014	notCor1	174	91.5	17942	51	21717
318	1880	ochPri0	569	101	138948	1065	1840608
319	2008	ochPri2	313	55	35317	1365	1110261
320	2012	ochPri3	1958	69	148238	1	499781
321	2012	octDeg1	2582	68	231489	1	464548
322	2013	odoRosDiv1	2581	68	180258	5	263661
323	2013	oncVol1	10	89.5	2046	1	18211
324	2014	opiHoa1	80	170.5	23360	1723.5	216549
325	2013	orcOrc1	2677	66	181922	5	357696
326	2011	oreNil1	1903	93	208888	2	734264
327	2007	ornAna1	793	49	70053	103	148119
328	2007	ornAna2	793	49	70053	103	148119
329	2012	oryAfe1	3595	65	293465	1	691489
330	2005	oryCun1	122	278.5	44566	462.5	91832
331	2009	oryCun2	12	44.5	836	446	9055
332	2006	oryLat1	141	144	25310	1	215389
333	2005	oryLat2	141	144	25310	1	253399
335	2011	otoGar3	3569	86	332700	39	663694
336	2010	oviAri1	5934	53	394316	37	1966190
337	2012	oviAri3	149	193	51933	215	178445
338	2015	oxyTri2	523	37	30028	5	25856
339	2013	panHod1	321	129	65178	1092	702884
340	2012	panPan1	63	133	11209	2	22114