bamvcf/musculus/bam/: bamvcf/musculus/vcf/: SN4570284_17073_AL16.sorted.nodups.realigned.recal.indels.vcf SN4570284_17073_AL16.sorted.nodups.realigned.recal.snps.vcf SN4570284_17074_AL19.sorted.nodups.realigned.recal.indels.vcf SN4570284_17074_AL19.sorted.nodups.realigned.recal.snps.vcf SN4570284_17075_AL33.sorted.nodups.realigned.recal.indels.vcf SN4570284_17075_AL33.sorted.nodups.realigned.recal.snps.vcf SN4570284_17076_AL38.sorted.nodups.realigned.recal.indels.vcf SN4570284_17076_AL38.sorted.nodups.realigned.recal.snps.vcf bamvcf/t-haplotype/MM9/: SN7640215_15831_SKU_147.merged.sorted.nodups.realigned.recal.indels.vcf SN7640215_15831_SKU_147.merged.sorted.nodups.realigned.recal.snps.filtered.vcf SN7640215_15831_SKU_147.samtools.mpileup.vcf newreads/domesticus_pop_transcriptomes/rawreads/: SN7640217_15764_CBBraintp1_1_sequence.fq.gz SN7640217_15764_CBBraintp1_2_sequence.fq.gz SN7640217_15765_CBBraintp121_1_sequence.fq.gz SN7640217_15765_CBBraintp121_2_sequence.fq.gz SN7640217_15766_CBBraintp172_1_sequence.fq.gz SN7640217_15766_CBBraintp172_2_sequence.fq.gz SN7640217_15767_CBBraintp3a2_1_sequence.fq.gz SN7640217_15767_CBBraintp3a2_2_sequence.fq.gz SN7640217_15768_CBBraintp4a_1_sequence.fq.gz SN7640217_15768_CBBraintp4a_2_sequence.fq.gz SN7640217_15769_CBBraintp51_1_sequence.fq.gz SN7640217_15769_CBBraintp51_2_sequence.fq.gz SN7640217_15770_CBBraintp710_1_sequence.fq.gz SN7640217_15770_CBBraintp710_2_sequence.fq.gz SN7640217_15771_CBBraintp81_1_sequence.fq.gz SN7640217_15771_CBBraintp81_2_sequence.fq.gz SN7640217_15772_CBGuttp1_1_sequence.fq.gz SN7640217_15772_CBGuttp1_2_sequence.fq.gz SN7640217_15773_CBGuttp121_1_sequence.fq.gz SN7640217_15773_CBGuttp121_2_sequence.fq.gz SN7640217_15774_IRSpleenIR121_1_sequence.fq.gz SN7640217_15774_IRSpleenIR121_2_sequence.fq.gz SN7640217_15800_CBGuttp4a_1_sequence.fq.gz SN7640217_15800_CBGuttp4a_2_sequence.fq.gz SN7640217_15801_CBGuttp81_1_sequence.fq.gz SN7640217_15801_CBGuttp81_2_sequence.fq.gz SN7640217_15802_CBHearttp1_1_sequence.fq.gz SN7640217_15802_CBHearttp1_2_sequence.fq.gz SN7640217_15803_CBHearttp121_1_sequence.fq.gz SN7640217_15803_CBHearttp121_2_sequence.fq.gz SN7640217_15804_CBHearttp172_1_sequence.fq.gz SN7640217_15804_CBHearttp172_2_sequence.fq.gz SN7640217_15805_CBHearttp3a2_1_sequence.fq.gz SN7640217_15805_CBHearttp3a2_2_sequence.fq.gz SN7640217_15806_CBHearttp4a_1_sequence.fq.gz SN7640217_15806_CBHearttp4a_2_sequence.fq.gz SN7640217_15807_CBHearttp51_1_sequence.fq.gz SN7640217_15807_CBHearttp51_2_sequence.fq.gz SN7640217_15808_CBHearttp710_1_sequence.fq.gz SN7640217_15808_CBHearttp710_2_sequence.fq.gz SN7640217_15809_CBHearttp81_1_sequence.fq.gz SN7640217_15809_CBHearttp81_2_sequence.fq.gz SN7640217_15810_CBKidneytp1_1_sequence.fq.gz SN7640217_15810_CBKidneytp1_2_sequence.fq.gz SN7640217_15811_CBKidneytp121_1_sequence.fq.gz SN7640217_15811_CBKidneytp121_2_sequence.fq.gz SN7640217_15812_CBKidneytp172_1_sequence.fq.gz SN7640217_15812_CBKidneytp172_2_sequence.fq.gz SN7640217_15813_CBKidneytp3a2_1_sequence.fq.gz SN7640217_15813_CBKidneytp3a2_2_sequence.fq.gz SN7640217_15814_CBMuscletp81_1_sequence.fq.gz SN7640217_15814_CBMuscletp81_2_sequence.fq.gz SN7640219_15913_CBSpleentp4a_1_sequence.fq.gz SN7640219_15913_CBSpleentp4a_2_sequence.fq.gz SN7640219_15914_CBSpleentp51_1_sequence.fq.gz SN7640219_15914_CBSpleentp51_2_sequence.fq.gz SN7640219_15915_CBSpleentp710_1_sequence.fq.gz SN7640219_15915_CBSpleentp710_2_sequence.fq.gz SN7640219_15916_CBSpleentp81_1_sequence.fq.gz SN7640219_15916_CBSpleentp81_2_sequence.fq.gz SN7640219_15917_CBTestistp1_1_sequence.fq.gz SN7640219_15917_CBTestistp1_2_sequence.fq.gz SN7640219_15918_CBTestistp121_1_sequence.fq.gz SN7640219_15918_CBTestistp121_2_sequence.fq.gz SN7640219_15919_CBTestistp172_1_sequence.fq.gz SN7640219_15919_CBTestistp172_2_sequence.fq.gz SN7640219_15920_CBTestistp3a2_1_sequence.fq.gz SN7640219_15920_CBTestistp3a2_2_sequence.fq.gz SN7640219_15930_CBTestistp4a_1_sequence.fq.gz SN7640219_15930_CBTestistp4a_2_sequence.fq.gz SN7640219_15931_CBTestistp51_1_sequence.fq.gz SN7640219_15931_CBTestistp51_2_sequence.fq.gz SN7640219_15932_CBTestistp710_1_sequence.fq.gz SN7640219_15932_CBTestistp710_2_sequence.fq.gz SN7640219_15933_CBTestistp81_1_sequence.fq.gz SN7640219_15933_CBTestistp81_2_sequence.fq.gz SN7640219_15934_CBThyroidtp1_1_sequence.fq.gz SN7640219_15934_CBThyroidtp1_2_sequence.fq.gz SN7640219_15935_CBThyroidtp121_1_sequence.fq.gz SN7640219_15935_CBThyroidtp121_2_sequence.fq.gz SN7640219_15936_MCThyroidE1b_1_sequence.fq.gz SN7640219_15936_MCThyroidE1b_2_sequence.fq.gz SN7640219_15945_CBThyroidtp172_1_sequence.fq.gz SN7640219_15945_CBThyroidtp172_2_sequence.fq.gz SN7640219_15946_CBThyroidtp3a2_1_sequence.fq.gz SN7640219_15946_CBThyroidtp3a2_2_sequence.fq.gz SN7640219_15947_CBThyroidtp4a_1_sequence.fq.gz SN7640219_15947_CBThyroidtp4a_2_sequence.fq.gz SN7640219_15948_CBThyroidtp710_1_sequence.fq.gz SN7640219_15948_CBThyroidtp710_2_sequence.fq.gz SN7640219_15949_CBThyroidtp81_1_sequence.fq.gz SN7640219_15949_CBThyroidtp81_2_sequence.fq.gz SN7640219_15950_IRBrain02FC_1_1_sequence.fq.gz SN7640219_15950_IRBrain02FC_1_2_sequence.fq.gz SN7640219_15951_IRBrain05F1C1_1_sequence.fq.gz SN7640219_15951_IRBrain05F1C1_2_sequence.fq.gz SN7640219_15952_IRBrain07F1C1_1_sequence.fq.gz SN7640219_15952_IRBrain07F1C1_2_sequence.fq.gz SN7640219_15962_IRBrain08F1_A_1_sequence.fq.gz SN7640219_15962_IRBrain08F1_A_2_sequence.fq.gz SN7640219_15963_IRBrain131_1_sequence.fq.gz SN7640219_15963_IRBrain131_2_sequence.fq.gz SN7640219_15964_IRBrain132_1_sequence.fq.gz SN7640219_15964_IRBrain132_2_sequence.fq.gz SN7640219_15965_IRBrainIR121_1_sequence.fq.gz SN7640219_15965_IRBrainIR121_2_sequence.fq.gz SN7640219_15966_IRBrainIR122_1_sequence.fq.gz SN7640219_15966_IRBrainIR122_2_sequence.fq.gz SN7640219_15967_IRGut02FC_1_1_sequence.fq.gz SN7640219_15967_IRGut02FC_1_2_sequence.fq.gz SN7640219_15968_MCThyroidC12_1_sequence.fq.gz SN7640219_15968_MCThyroidC12_2_sequence.fq.gz SN7640219_15976_IRGut05F1C1_1_sequence.fq.gz SN7640219_15976_IRGut05F1C1_2_sequence.fq.gz SN7640219_15977_IRGut07F1C1_1_sequence.fq.gz SN7640219_15977_IRGut07F1C1_2_sequence.fq.gz SN7640219_15978_IRGut08F1_A_1_sequence.fq.gz SN7640219_15978_IRGut08F1_A_2_sequence.fq.gz SN7640219_15979_IRGut131_1_sequence.fq.gz SN7640219_15979_IRGut131_2_sequence.fq.gz SN7640219_15980_IRGut132_1_sequence.fq.gz SN7640219_15980_IRGut132_2_sequence.fq.gz SN7640219_15981_IRGutIR121_1_sequence.fq.gz SN7640219_15981_IRGutIR121_2_sequence.fq.gz SN7640219_15982_IRGutIR122_1_sequence.fq.gz SN7640219_15982_IRGutIR122_2_sequence.fq.gz SN7640219_15983_IRHeart02FC_1_1_sequence.fq.gz SN7640219_15983_IRHeart02FC_1_2_sequence.fq.gz SN7640219_15993_IRHeart05F1C1_1_sequence.fq.gz SN7640219_15993_IRHeart05F1C1_2_sequence.fq.gz SN7640219_15994_IRHeart07F1C1_1_sequence.fq.gz SN7640219_15994_IRHeart07F1C1_2_sequence.fq.gz SN7640219_15995_IRHeart08F1_A_1_sequence.fq.gz SN7640219_15995_IRHeart08F1_A_2_sequence.fq.gz SN7640219_15996_IRHeart131_1_sequence.fq.gz SN7640219_15996_IRHeart131_2_sequence.fq.gz SN7640219_15997_IRHeart132_1_sequence.fq.gz SN7640219_15997_IRHeart132_2_sequence.fq.gz SN7640219_15998_IRHeartIR121_1_sequence.fq.gz SN7640219_15998_IRHeartIR121_2_sequence.fq.gz SN7640219_15999_MCThyroidB2C_1_sequence.fq.gz SN7640219_15999_MCThyroidB2C_2_sequence.fq.gz SN7640219_16007_IRHeartIR122_1_sequence.fq.gz SN7640219_16007_IRHeartIR122_2_sequence.fq.gz SN7640219_16008_IRKidney02FC_1_1_sequence.fq.gz SN7640219_16008_IRKidney02FC_1_2_sequence.fq.gz SN7640219_16009_IRKidney05F1C1_1_sequence.fq.gz SN7640219_16009_IRKidney05F1C1_2_sequence.fq.gz SN7640219_16010_IRKidney07F1C1_1_sequence.fq.gz SN7640219_16010_IRKidney07F1C1_2_sequence.fq.gz SN7640219_16011_IRKidney08F1_A_1_sequence.fq.gz SN7640219_16011_IRKidney08F1_A_2_sequence.fq.gz SN7640219_16012_IRKidney131_1_sequence.fq.gz SN7640219_16012_IRKidney131_2_sequence.fq.gz SN7640219_16013_IRKidney132_1_sequence.fq.gz SN7640219_16013_IRKidney132_2_sequence.fq.gz SN7640219_16014_IRKidneyIR121_1_sequence.fq.gz SN7640219_16014_IRKidneyIR121_2_sequence.fq.gz SN7640219_16024_IRKidneyIR122_1_sequence.fq.gz SN7640219_16024_IRKidneyIR122_2_sequence.fq.gz SN7640219_16025_IRLiver02FC_1_1_sequence.fq.gz SN7640219_16025_IRLiver02FC_1_2_sequence.fq.gz SN7640219_16026_IRLiver05F1C1_1_sequence.fq.gz SN7640219_16026_IRLiver05F1C1_2_sequence.fq.gz SN7640219_16027_IRLiver07F1C1_1_sequence.fq.gz SN7640219_16027_IRLiver07F1C1_2_sequence.fq.gz SN7640219_16028_IRLiver08F1_A_1_sequence.fq.gz SN7640219_16028_IRLiver08F1_A_2_sequence.fq.gz SN7640219_16029_IRLiver131_1_sequence.fq.gz SN7640219_16029_IRLiver131_2_sequence.fq.gz SN7640219_16030_MCThyroid18b_1_sequence.fq.gz SN7640219_16030_MCThyroid18b_2_sequence.fq.gz SN7640222_16529_CBKidneytp4a_1_sequence.fq.gz SN7640222_16529_CBKidneytp4a_2_sequence.fq.gz SN7640222_16530_CBKidneytp51_1_sequence.fq.gz SN7640222_16530_CBKidneytp51_2_sequence.fq.gz SN7640222_16531_CBKidneytp710_1_sequence.fq.gz SN7640222_16531_CBKidneytp710_2_sequence.fq.gz SN7640222_16532_CBKidneytp81_1_sequence.fq.gz SN7640222_16532_CBKidneytp81_2_sequence.fq.gz SN7640222_16533_CBLivertp1_1_sequence.fq.gz SN7640222_16533_CBLivertp1_2_sequence.fq.gz SN7640222_16534_MCTestis15b_1_sequence.fq.gz SN7640222_16534_MCTestis15b_2_sequence.fq.gz SN7640222_16535_MCTestis16b_1_sequence.fq.gz SN7640222_16535_MCTestis16b_2_sequence.fq.gz SN7640222_16536_CBLivertp3a2_1_sequence.fq.gz SN7640222_16536_CBLivertp3a2_2_sequence.fq.gz SN7640222_16546_CBLivertp4a_1_sequence.fq.gz SN7640222_16546_CBLivertp4a_2_sequence.fq.gz SN7640222_16547_CBLivertp51_1_sequence.fq.gz SN7640222_16547_CBLivertp51_2_sequence.fq.gz SN7640222_16548_CBLivertp710_1_sequence.fq.gz SN7640222_16548_CBLivertp710_2_sequence.fq.gz SN7640222_16549_CBLivertp81_1_sequence.fq.gz SN7640222_16549_CBLivertp81_2_sequence.fq.gz SN7640222_16550_CBLungtp1_1_sequence.fq.gz SN7640222_16550_CBLungtp1_2_sequence.fq.gz SN7640222_16551_CBLungtp121_1_sequence.fq.gz SN7640222_16551_CBLungtp121_2_sequence.fq.gz SN7640222_16552_CBTHYTP51_1_sequence.fq.gz SN7640222_16552_CBTHYTP51_2_sequence.fq.gz SN7640222_16560_CBLungtp172_1_sequence.fq.gz SN7640222_16560_CBLungtp172_2_sequence.fq.gz SN7640222_16561_CBLungtp3a2_1_sequence.fq.gz SN7640222_16561_CBLungtp3a2_2_sequence.fq.gz SN7640222_16562_CBLungtp51_1_sequence.fq.gz SN7640222_16562_CBLungtp51_2_sequence.fq.gz SN7640222_16563_CBLungtp81_1_sequence.fq.gz SN7640222_16563_CBLungtp81_2_sequence.fq.gz SN7640222_16564_CBMuscletp1_1_sequence.fq.gz SN7640222_16564_CBMuscletp1_2_sequence.fq.gz SN7640222_16565_MCTestis18b_1_sequence.fq.gz SN7640222_16565_MCTestis18b_2_sequence.fq.gz SN7640222_16566_CBMuscletp3a2_1_sequence.fq.gz SN7640222_16566_CBMuscletp3a2_2_sequence.fq.gz SN7640222_16567_CBMuscletp4a_1_sequence.fq.gz SN7640222_16567_CBMuscletp4a_2_sequence.fq.gz SN7640222_16577_CBMuscletp51_1_sequence.fq.gz SN7640222_16577_CBMuscletp51_2_sequence.fq.gz SN7640222_16578_CBMuscletp710_1_sequence.fq.gz SN7640222_16578_CBMuscletp710_2_sequence.fq.gz SN7640222_16579_CBSpleentp1_1_sequence.fq.gz SN7640222_16579_CBSpleentp1_2_sequence.fq.gz SN7640222_16580_CBSpleentp121_1_sequence.fq.gz SN7640222_16580_CBSpleentp121_2_sequence.fq.gz SN7640222_16581_CBSpleentp172_1_sequence.fq.gz SN7640222_16581_CBSpleentp172_2_sequence.fq.gz SN7640222_16582_CBSpleentp3a2_1_sequence.fq.gz SN7640222_16582_CBSpleentp3a2_2_sequence.fq.gz SN7640222_16583_MCThyroidF1B_1_sequence.fq.gz SN7640222_16583_MCThyroidF1B_2_sequence.fq.gz SN7640224_16591_IRLiver132_1_sequence.fq.gz SN7640224_16591_IRLiver132_2_sequence.fq.gz SN7640224_16592_IRLiverIR121_1_sequence.fq.gz SN7640224_16592_IRLiverIR121_2_sequence.fq.gz SN7640224_16593_IRLiverIR122_1_sequence.fq.gz SN7640224_16593_IRLiverIR122_2_sequence.fq.gz SN7640224_16594_IRLung02FC_1_1_sequence.fq.gz SN7640224_16594_IRLung02FC_1_2_sequence.fq.gz SN7640224_16595_IRLung05F1C1_1_sequence.fq.gz SN7640224_16595_IRLung05F1C1_2_sequence.fq.gz SN7640224_16596_IRLung07F1C1_1_sequence.fq.gz SN7640224_16596_IRLung07F1C1_2_sequence.fq.gz SN7640224_16597_IRLung08F1_A_1_sequence.fq.gz SN7640224_16597_IRLung08F1_A_2_sequence.fq.gz SN7640224_16598_IRLung131_1_sequence.fq.gz SN7640224_16598_IRLung131_2_sequence.fq.gz SN7640224_16608_IRLung132_1_sequence.fq.gz SN7640224_16608_IRLung132_2_sequence.fq.gz SN7640224_16609_IRLungIR121_1_sequence.fq.gz SN7640224_16609_IRLungIR121_2_sequence.fq.gz SN7640224_16610_IRLungIR122_1_sequence.fq.gz SN7640224_16610_IRLungIR122_2_sequence.fq.gz SN7640224_16611_IRMuscle02FC_1_1_sequence.fq.gz SN7640224_16611_IRMuscle02FC_1_2_sequence.fq.gz SN7640224_16612_IRMuscle05F1C1_1_sequence.fq.gz SN7640224_16612_IRMuscle05F1C1_2_sequence.fq.gz SN7640224_16613_IRMuscle07F1C1_1_sequence.fq.gz SN7640224_16613_IRMuscle07F1C1_2_sequence.fq.gz SN7640224_16614_MCThyroid16b_1_sequence.fq.gz SN7640224_16614_MCThyroid16b_2_sequence.fq.gz SN7640224_16765_IRMuscle08F1_A_1_sequence.fq.gz SN7640224_16765_IRMuscle08F1_A_2_sequence.fq.gz SN7640224_16766_IRMuscle131_1_sequence.fq.gz SN7640224_16766_IRMuscle131_2_sequence.fq.gz SN7640224_16767_IRMuscle132_1_sequence.fq.gz SN7640224_16767_IRMuscle132_2_sequence.fq.gz SN7640224_16768_IRMuscleIR122_1_sequence.fq.gz SN7640224_16768_IRMuscleIR122_2_sequence.fq.gz SN7640224_16769_IRSpleen02FC_1_1_sequence.fq.gz SN7640224_16769_IRSpleen02FC_1_2_sequence.fq.gz SN7640224_16770_IRSpleen08F1_A_1_sequence.fq.gz SN7640224_16770_IRSpleen08F1_A_2_sequence.fq.gz SN7640224_16771_IRSpleen131_1_sequence.fq.gz SN7640224_16771_IRSpleen131_2_sequence.fq.gz SN7640224_16772_IRSpleen132_1_sequence.fq.gz SN7640224_16772_IRSpleen132_2_sequence.fq.gz SN7640224_16799_IRSpleenIR122_1_sequence.fq.gz SN7640224_16799_IRSpleenIR122_2_sequence.fq.gz SN7640224_16800_IRTestis02FC_1_1_sequence.fq.gz 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SN7640224_16819_IRThyroid07F1C1_1_sequence.fq.gz SN7640224_16819_IRThyroid07F1C1_2_sequence.fq.gz SN7640224_16820_IRThyroid08F1_A_1_sequence.fq.gz SN7640224_16820_IRThyroid08F1_A_2_sequence.fq.gz SN7640224_16821_IRThyroid131_1_sequence.fq.gz SN7640224_16821_IRThyroid131_2_sequence.fq.gz SN7640224_16830_IRThyroid132_1_sequence.fq.gz SN7640224_16830_IRThyroid132_2_sequence.fq.gz SN7640224_16831_IRThyroidIR121_1_sequence.fq.gz SN7640224_16831_IRThyroidIR121_2_sequence.fq.gz SN7640224_16832_IRThyroidIR122_1_sequence.fq.gz SN7640224_16832_IRThyroidIR122_2_sequence.fq.gz SN7640224_16833_MCBrain14_1_sequence.fq.gz SN7640224_16833_MCBrain14_2_sequence.fq.gz SN7640224_16834_MCBrain15b_1_sequence.fq.gz SN7640224_16834_MCBrain15b_2_sequence.fq.gz SN7640224_16835_MCBrain16b_1_sequence.fq.gz SN7640224_16835_MCBrain16b_2_sequence.fq.gz SN7640224_16836_MCThyroid14_1_sequence.fq.gz SN7640224_16836_MCThyroid14_2_sequence.fq.gz SN7640224_16845_MCBrain18b_1_sequence.fq.gz 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SN7640173_9424_Apo_2_sequence.fq.gz SN7640173_9425_Mat2_1_sequence.fq.gz SN7640173_9425_Mat2_2_sequence.fq.gz SN7640173_9426_Scl_1_sequence.fq.gz SN7640173_9426_Scl_2_sequence.fq.gz newreads/wildmouse_transcriptomes/bigWigs/: AH_B.bw AH_L.bw AH_T.bw AP_B.bw AP_L.bw AP_T.bw CB_B.bw CB_L.bw CB_T.bw KH_B.bw KH_L.bw KH_T.bw MA_B.bw MA_L.bw MA_T.bw MC_B.bw MC_L.bw MC_T.bw SC_B.bw SC_L.bw SC_T.bw SP_B.bw SP_L.bw SP_T.bw TA_B.bw TA_L.bw TA_T.bw WI_B.bw WI_L.bw WI_T.bw newreads/wildmouse_transcriptomes/contigs/: AH.transcripts AP.transcripts CB.transcripts KH.transcripts MA.transcripts MC.transcripts SC.transcripts SP.transcripts TA.transcripts WI.transcripts newreads/wildmouse_transcriptomes/reads/: AH_B_1.gz AH_B_1.readcount.gz AH_B_2.gz AH_B_2.readcount.gz AH_B_SE.gz AH_L_1.gz AH_L_1.readcount.gz AH_L_2.gz AH_L_2.readcount.gz AH_L_SE.gz AH_T_1.gz AH_T_2.gz AH_T_SE.gz AP_B_1.gz AP_B_1.readcount.gz AP_B_2.gz AP_B_2.readcount.gz AP_B_SE.gz AP_L_1.gz AP_L_1.readcount.gz AP_L_2.gz 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