Table 3 Analysis of 23 selected de novo deletions
StrainChrStartEndSize (kb)Start (refined with BWT)End (refined with BWT)Size (refined with BWT)HaplotypeGenesRegulatory ElementsOverlaps with known SVNotes
CC0042116,465,000116,480,00015NDNDNDWSB/EiJNoneNoneYesRepeat
CC0041875,868,00075,896,0002875,863,98575,900,55136,566C57BL/6JZbtb7c (intron)ENSMUSR00000378576, ENSMUSR00000378577, ENSMUSR00000378578YesUnique, splice site
CC006236,341,00036,366,00025NDNDNDPWK/PhJNoneENSMUSR00000152903YesOlfactory receptor cluster
CC0071353,304,00053,318,0001453,299,89253,322,38322,491NOD/ShiLtJNoneENSMUSR00000074496, ENSMUSR00000339964, ENSMUSR00000074498, ENSMUSR00000339965, ENSMUSR00000074500NoMicrohomology
CC0081659,216,00059,261,00045NDNDNDPWK/PhJOlfr199 (partial), Olfr200-ps1ENSMUSR00000114105Yes
CC0111870,254,00070,257,000370,249,78570,260,63610,851A/JNoneENSMUSR00000378203NoUnique
CC0136124,529,000124,569,00040NDNDNDPWK/PhJ to WSB/EiJ transitionC1s1ENSMUSR00000235398, ENSMUSR00000439605, ENSMUSR00000235399, ENSMUSR00000439609, ENSMUSR00000439610YesComplex SD
CC0251211,617,00011,621,000411,613,04411,625,41212,368PWK/PhJNoneNoneYes
CC0261757,161,00057,245,0008057,148,21257,248,753100,541C57BL/6JCd70, Tnsf14, C3, mir6978, Gpr108ManyYesMicrohomology
CC030843,624,00043,626,0002NDNDNDPWK/PhJGm5346 (partial)NoneYes
CC038286,260,00086,266,0006NDNDNDCAST/EiJNoneNoneYesOlfactory receptor cluster
CC043490,613,00090,621,0008NDNDNDNOD/ShiLtJNoneNoneNo
CC0465151,538,000151,547,0009NDNDNDCAST/EiJVmn2r-ps26 (partial)NoneYes
CC0553132,902,000132,939,00037132,897,360132,944,51047,150129S1/SvImjNpnt (partial)ManyNoMicrohomology
CC056855,080,00055,094,00014NDNDNDPWK/PhJGm8734NoneYes
CC0571670,377,00070,378,000170,377,00070,392,21215,212C57BL/6JGbe1 (intron)NoneYesProximal end overlaps with repeat
CC072611,664,00011,738,00074NDNDNDWSB/EiJNoneENSMUSR00000431623, ENSMUSR00000222992, ENSMUSR00000222993,Yes
CC0721540,549,00040,551,000240,544,59840,555,61411,016129S1/SvImjNoneNoneNoMicrosatellite
CC0741324,536,00024,539,000324,529,80024,543,00013,200PWK/PhJNoneENSMUSR00000337301, ENSMUSR00000070027YesEnds overlap with repeats. No exact breakpoints determined
CC0741327,113,00027,123,00010NDNDNDPWK/PhJPrl3d2 (partial)NoneYes
CC0741333,303,00033,304,0001NDNDNDPWK/PhJNoneNoneYes
CC0754112,022,000112,031,0009NDNDNDWSB/EiJSkint1 (partial)NoneYes
CC075927,720,00027,731,00011NDNDNDCAST/EiJNoneENSMUSR00000462205No
  • The table provides the strain and the start and positions of the initial discovery step and the refinement step by BWT when applicable. It also indicates the founder haplotype, gene and regulatory content as obtained from Ensembl (v87). Finally, the table indicates whether the deletion overlaps with a known structural variant (SV) and defining characteristics. ND, not determined.