I was finally able to download the BAM file of the high-quality Altai Neanderthal sequence. It is available as accession ERP002097 at the European Nucleotide Archive <http://www.ebi.ac.uk/ena/data/view/ERP002097>. It actually consists of 5 BAM files, but so far I have only downloaded the first of these, a 12.3-gB file covering about chromosomes 1-6. To download it I used the free FlashGet Download Manager and set my Control Panel power option to "never sleep" to prevent the computer from going to sleep and suspending the download. The download required about 44 hours, but worked well. I can now view this Neanderthal BAM file against my own FGC WGS BAM file using the free Golden Helix Browser. The Altai Neanderthal sequence is almost complete with just a few gaps, much better than the Vindija Neanderthal sequences (from the site in Croatia), which can be seen in the UCSC Browser. There are some 200-300 SNPs in the region of the PRDM2 gene on chr 1 which I clearly share with the Altai Neanderthal individual. Most of these have a frequency in the modern human population of from 0.03 to 0.05 and for most of these the Altai sequence is homozygous while I am heterozygous. Most of these SNPS are present in Europeans at a level of about 2%, in South Asians at a level of 12-14%, and in East Asians at a level of about 2% (from 1000 Genomes data). However, there is a subset of the above SNPs which have a modern human frequency of about 0.013-0.014 and are present only in Europeans and South Asians, but not in East Asians. These rarer SNPs are still present in Europeans at a level of about 2%, indicating that the Neanderthal ancestors of most Europeans had all of these SNPs, while for South Asians the frequency of these rarer SNPs drops to about 4.6% compared to the 12-14% for the more common SNPs, indicating a more varied group of Neanderthal ancestors for South Asians. I am pasting a table below showing the rs numbers and locations of these rarer Neanderthal SNPs. This table also shows whether or not the Altai and Vindija Neanderthal sequences have these SNPs. It can be seen that there is a lot of variability, some of these SNPs being homozygous, some heterozygous, and some not present at all in the Altai and Vindija sequences. It will be interesting to see if a Neanderthal fossil will eventually be found sharing all of these rarer (more downstream?) SNPs. This would help to pinpoint the location of the Neanderthal introgression into modern Europeans. NEANDERTHAL SNPs FOUND ONLY IN EUROPEANS AND SOUTH ASIANS BUT NOT EAST ASIANS (OR AFRICANS) [chr1;Build GRCh37; all have overall freq=.013778 unless otherwise indicated] EUR=European; EAS=East Asian including Chinese, Vietnamese, and Japanese; SAS=South Asian including Bengali, Gujariti Indian, Sri Lankan Tamil, and Punjabi; YRI=Yoruba from Nigeria; NC= not covered SNP Location Alleles Neanderthal reads Frequencies in modern humans Altai Vindija rs369433490 at 13985244 C to T 2C 4C (overall freq=.0129792; EUR .0169, EAS 0, SAS.047, YRI 0) rs116573139 at 14009444 C to A 2C 1A (EUR .0209, EAS 0, SAS .046, YRI 0) rs115905418 at 14015398 A to G 1A1G 1A2G (EUR .0209, EAS 0, SAS .046, YRI 0) rs181956703 at 14032408 C to T 3C NC (EUR .0209, EAS 0, SAS .046, YRI 0) rs141008778 at 14035290 G to A 3G2A 3G2A (EUR .0290, EAS 0, SAS .046, YRI 0) rs114155321 at 14037619 G to T 2G NC (EUR .0209, EAS 0, SAS .046, YRI 0) rs114005658 at 14044716 G to T 4G2T 1G (overall freq=.0135783; EUR .0209, EAS 0, SAS .045, YRI 0) rs114497926 at 14045457 T to C 2T3C 3T (EUR .0209, EAS 0, SAS .046, YRI 0) rs115494198 at 14047679 G to A 7G 3G (EUR .0209, EAS 0, SAS .046, YRI 0) rs115717211 at 14050333 C to T 3T 3C (EUR .0209, EAS 0, SAS .046, YRI 0) rs114228377 at 14053534 T to G 1T1G 3T1G (EUR .0209, EAS 0, SAS .046, YRI 0) rs116572816 at 14064321 A to G 3A 2A (overall freq=.0139776; EUR .0209, EAS 0, SAS .046, YRI 0) rs115723647 at 14067102 C to T 2C NC (EUR .0209, EAS 0, SAS .046, YRI 0) rs114514035 at 14075112 C to A 3C 4C1A (EUR .0209, EAS 0, SAS .046, YRI 0) rs115824810 at 14081298 G to A 2A 1G (EUR .0209, EAS 0, SAS .046, YRI 0) rs114036986 at 14082000 T to A 4T NC (EUR .0209, EAS 0, SAS .046, YRI 0) rs115231513 at 14083712 A to T 2A NC (EUR .0209, EAS 0, SAS .046, YRI 0) rs187588348 at 14084745 C to T 3T 4C1T (EUR .0209, EAS 0, SAS .046, YRI 0) rs115718893 at 14089057 T to A 3T 1T (EUR .0209, EAS 0, SAS .046, YRI 0) rs114100510 at 14089729 A to G 6G 1G (EUR .0209, EAS 0, SAS .046, YRI 0) rs114782786 at 14092651 C to T 2C 2C (EUR .0209, EAS 0, SAS .046, YRI 0) rs116636384 at 14102245 T to C 2T 2T1C (overall freq=.0127796; EUR .0169, EAS 0, SAS .046, YRI 0) rs75266213 at 14102539 T to A 3A 2A (overall freq=.0127796; EUR .0169, EAS 0, SAS .046, YRI 0) rs114937447 at 14114988 A to C 4A NC (overall freq=.0127796; EUR .0169, EAS 0, SAS .046, YRI 0) rs114103649 at 14117543 C to G 2C 1C1G (overall freq=.0127796; EUR .0169, EAS 0, SAS .046, YRI 0) rs114857261 at 14126873 G to T 2G 3G1T (overall freq=.0171725; EUR .0169, EAS 0, SAS .0685, YRI 0)