Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family

Table 1 BAC insert assemblies based on Illumina and PacBio reads

Accession number	BAC clone	Cluster^a	Sequencing technique^b	No. of contigs	Length (nt)	Final length^c	Gaps^d	N50 (nt)	Comments
KU668451	10B1	1	Illumina	1	153857		8	153857	Both ends confirmed
KU668451	10B1	1	PacBio	1	166299	157472	0	166299
KU668452	4074J14	1	Illumina	1	136199		8	136199	Both ends confirmed
KU668452	4074J14	1	PacBio	1	151419	142396	0	151419	Artificial duplication at the ends
KU668453	10K9	2	Illumina	1	148572		2	148572	Both ends confirmed
KU668453	10K9	2	PacBio	1	153438	144627	0	153438	Artificial duplication at the ends
KU668450	10M18	3	Illumina	1	122168		8	122168	Both ends confirmed
KU668450	10M18	3	PacBio	1	136808	74402	0	136808
KU668454	3104P4	3	Illumina	1	118285		7	118285	Both ends confirmed
KU668454	3104P4	3	PacBio	1	127392	118584	0	127392	Artificial duplication at one end
Not submitted	14K16	1″	Illumina	5	99921		3	58593	Ends missing
Not submitted	3020I13	SB^+e	Illumina	1	56106		0	56106	Finished, both ends confirmed
Not submitted	4024N22	2	Illumina	7	293347		31	77201	One end missing
Not submitted	4069G2	SB⁺	Illumina	10	125037		2	54882	Both ends confirmed
Not submitted	4069C2	SB⁺	Illumina	24	27398		0	1016	Very poor assembly, one end missing
Not submitted	4092O3	2′	Illumina	6	279956		7	125559	Both ends missing

^aSee Fig. 2
^bBACs sequenced by both techniques were used to characterize the Sp185/333 gene family structure
^cFinal length was determined after corrections to remove artificial repeats generated from the assembly process and vector contamination
^dGaps are defined as spaces in the assemblies with unknown nucleotides that are indicated in the sequence as Ns
^eSB⁺; positive for Sp185/333 sequences by Southern blot (see Additional file 3: Figure S2B)

ISSN: 1471-2164