Molecular archeology of L1 insertions in the human genome

Table 1 Dataset characteristics and summary of TSDfinder results

Chromosome	Total Mb sequenced^*	Estimated chromosome length (Mb)	Sequence completed	Number of 3' intact insertion events^†	Number of 3'-intact per Mb sequenced	Number with TSDs	Standard insertion	3' Trans duction^‡	Number with TSDs/Mb sequenced	Total number of FL L1s^§	Percentage of 3' intact that are FL	Density of FL L1s/Mb sequenced
1	230.3	252.5	91%	5,123	22.2	1,195	756	439	5.2	258	5%	1.12
2	226.5	238.0	95%	5,597	24.7	1,302	807	495	5.7	279	5%	1.23
3	192.0	204.4	94%	5,064	26.4	1,087	680	407	5.7	223	4%	1.16
4	175.9	189.6	93%	5,433	30.9	1,094	684	410	6.2	240	4%	1.36
5	169.2	180.5	94%	4,852	28.7	1,049	651	398	6.2	259	5%	1.53
6	173.4	178.1	97%	4,734	27.3	1,089	692	397	6.3	254	5%	1.46
7	153.8	160.4	96%	3,734	24.3	829	499	330	5.4	201	5%	1.31
8	134.8	143.4	94%	3,586	26.6	816	519	297	6.1	215	6%	1.59
9	114.7	131.7	87%	2,735	23.9	660	418	242	5.8	143	5%	1.25
10	134.7	139.7	96%	3,048	22.6	687	422	265	5.1	163	5%	1.21
11	139.1	141.2	99%	3,675	26.4	795	515	280	5.7	199	5%	1.43
12	130.2	138.4	94%	3,317	25.5	740	462	278	5.7	186	6%	1.43
13	99.1	116.7	85%	2,596	26.2	583	360	223	5.9	97	4%	0.98
14	89.0	105.4	84%	2,173	24.4	502	307	195	5.6	128	6%	1.44
15	80.7	98.9	82%	1,644	20.4	417	253	164	5.2	92	6%	1.14
16	77.6	92.6	84%	1,399	18.0	313	188	125	4.0	50	4%	0.64
17	81.3	83.3	98%	1,256	15.4	313	196	117	3.8	30	2%	0.37
18	79.8	81.3	98%	1,908	23.9	446	278	168	5.6	86	5%	1.08
19	58.6	77.1	76%	730	12.5	189	113	76	3.2	32	4%	0.55
20	60.4	61.8	98%	1,003	16.6	255	163	92	4.2	46	5%	0.76
21	33.9	46.2	73%	821	24.3	195	121	74	5.8	17	2%	0.50
22	34.8	47.2	74%	422	12.1	108	57	51	3.1	19	5%	0.55
X	141.1	150.3	94%	6,067	43.0	1,345	811	534	9.5	336	6%	2.38
Y	22.7	59.0	39%	959	42.2	210	108	102	9.2	93	10%	4.09
Un^¶	8.9	0.0		272	30.5	47	28	19	5.3	11	4%	1.23
Total	2,842.6	3,117.8	91%	72,148		16,266	10,088	6,178		3,657

^*The total amount of sequence (nucleotides) available on 29 August 2001 for each chromosome is indicated. ^†The 3' intact L1s must not have more than a 30-nucleotide deletion from the 3' end. ^‡If the sequence between the start of the poly(A) tail and the 3' end of the annotated L1 exceeded 30 nucleotides, the L1 was classified as a 3' transduction candidate. ^§ Full-length (FL) L1s must have an intact 3' end and no more than a 10-nucleotide deletion at the 5' end; we did not require this set of full-length L1s to have TSDs. ^¶ Un, unknown chromosome localization as reported in the NCBI contigs resource.

ISSN: 1474-760X