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Thread: Autosomal of Egyptian pharaohs?

  1. #1
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    Autosomal of Egyptian pharaohs?

    Last edited by David Bush; 10-12-2020 at 09:21 AM.

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  3. #2
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    Could those shotguns be autosomal data? They don't explicitly state to be y or mtDNA and are pretty big.

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  5. #3
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    It indeed seems to be autosomal data! Yleaf gives this output for the sample NAII against hg19:
    Code:
    chr	reads	perc
    chr1	59962	7.97%
    chr10	43668	5.8%
    chr11	33899	4.5%
    chr11_gl000202_random	7	0.0%
    chr12	33039	4.39%
    chr13	23863	3.17%
    chr14	22264	2.96%
    chr15	20264	2.69%
    chr16	27037	3.59%
    chr17	19866	2.64%
    chr17_ctg5_hap1	181	0.02%
    chr17_gl000203_random	16	0.0%
    chr17_gl000204_random	10	0.0%
    chr17_gl000205_random	139	0.02%
    chr17_gl000206_random	3	0.0%
    chr18	19394	2.58%
    chr18_gl000207_random	0	0.0%
    chr19	15707	2.09%
    chr19_gl000208_random	284	0.04%
    chr19_gl000209_random	19	0.0%
    chr1_gl000191_random	14	0.0%
    chr1_gl000192_random	142	0.02%
    chr2	62685	8.33%
    chr20	14829	1.97%
    chr21	9891	1.31%
    chr21_gl000210_random	3	0.0%
    chr22	8825	1.17%
    chr3	48827	6.49%
    chr4	49246	6.54%
    chr4_ctg9_hap1	72	0.01%
    chr4_gl000193_random	138	0.02%
    chr4_gl000194_random	82	0.01%
    chr5	45031	5.98%
    chr6	42320	5.62%
    chr6_apd_hap1	101	0.01%
    chr6_cox_hap2	255	0.03%
    chr6_dbb_hap3	218	0.03%
    chr6_mann_hap4	198	0.03%
    chr6_mcf_hap5	167	0.02%
    chr6_qbl_hap6	193	0.03%
    chr6_ssto_hap7	185	0.02%
    chr7	40588	5.39%
    chr7_gl000195_random	166	0.02%
    chr8	37258	4.95%
    chr8_gl000196_random	4	0.0%
    chr8_gl000197_random	1	0.0%
    chr9	30328	4.03%
    chr9_gl000198_random	70	0.01%
    chr9_gl000199_random	2513	0.33%
    chr9_gl000200_random	20	0.0%
    chr9_gl000201_random	4	0.0%
    chrM	382	0.05%
    chrUn_gl000211	50	0.01%
    chrUn_gl000212	153	0.02%
    chrUn_gl000213	26	0.0%
    chrUn_gl000214	260	0.03%
    chrUn_gl000215	20	0.0%
    chrUn_gl000216	736	0.1%
    chrUn_gl000217	48	0.01%
    chrUn_gl000218	82	0.01%
    chrUn_gl000219	157	0.02%
    chrUn_gl000220	3000	0.4%
    chrUn_gl000221	89	0.01%
    chrUn_gl000222	50	0.01%
    chrUn_gl000223	31	0.0%
    chrUn_gl000224	270	0.04%
    chrUn_gl000225	493	0.07%
    chrUn_gl000226	1812	0.24%
    chrUn_gl000227	29	0.0%
    chrUn_gl000228	77	0.01%
    chrUn_gl000229	15	0.0%
    chrUn_gl000230	6	0.0%
    chrUn_gl000231	24	0.0%
    chrUn_gl000232	39	0.01%
    chrUn_gl000233	14	0.0%
    chrUn_gl000234	28	0.0%
    chrUn_gl000235	24	0.0%
    chrUn_gl000236	11	0.0%
    chrUn_gl000237	36	0.0%
    chrUn_gl000238	3	0.0%
    chrUn_gl000239	21	0.0%
    chrUn_gl000240	24	0.0%
    chrUn_gl000241	36	0.0%
    chrUn_gl000242	6	0.0%
    chrUn_gl000243	26	0.0%
    chrUn_gl000244	13	0.0%
    chrUn_gl000245	13	0.0%
    chrUn_gl000246	4	0.0%
    chrUn_gl000247	10	0.0%
    chrUn_gl000248	3	0.0%
    chrUn_gl000249	2	0.0%
    chrX	22624	3.01%
    chrY	8045	1.07%
    *	0	0.0%
    About 700 thousand reads. Yleaf does produce a BAM file, but I'm not sure if it's good for further analysis. Should HG38 be used?

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  7. #4
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    Supposed that MTA is using the Egyptian auDNA Data of this Study in their Database.

    Autosomal using ancient populations :
    93% Late Period Ancient Egyptian, 4% JOR_EBA, 3% GRC_Minoan_Lassithi (Just another G25's Scaled results with a Suitable fit).

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    I don't know how to properly handle .fastq to plink .bed, but if someone could, then we could get G25 coordinates to mess around with.

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  11. #6
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    Maybe Vadim Verenich could help. He did some conversions for the Viking samples.
    Ελευθερία ή θάνατος.

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  13. #7
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    I checked Y SNP
    Most likely it was H2

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    Quote Originally Posted by Michalis Moriopoulos View Post
    Maybe Vadim Verenich could help. He did some conversions for the Viking samples.
    Thanks. Are his Viking conversions accessible? How do you contact Vadim?

    Viking autosomal samples would be perfect for something which I am working on.

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    Quote Originally Posted by C J Wyatt III View Post
    Thanks. Are his Viking conversions accessible? How do you contact Vadim?

    Viking autosomal samples would be perfect for something which I am working on.
    He's a member here; you can search for him. The Viking samples are in the Global 25 now.
    Ελευθερία ή θάνατος.

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  19. #10
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    I am creating BAMs from the shotguns (ERR1937835 and ERR1937832) with EAGER2.

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