Y-SNP calls for Harney (2020): A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Tagged: Ekven, H2, Hungary, I1, Q1a, Q1b, R-L151, R-Z283, R-Z93, R1a, Volosovo

This topic has 1 reply, 1 voice, and was last updated 2 years, 8 months ago by .

Viewing 2 posts - 1 through 2 (of 2 total)

Author

Posts
December 22, 2020 at 2:52 pm #34529
Carlos Quiles
Keymaster
Harney, É., Cheronet, O., Fernandes, D. M., Sirak, K., Mah, M., Bernardos, R., … & Oppenheimer, J. (2020). A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth. bioRxiv

https://doi.org/10.1101/2020.08.19.256412

Abstract:

Ancient DNA sampling methods—although optimized for efficient DNA extraction—are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but standard destructive sampling methods often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and 9 corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Accession number: PRJEB32750

Batch Y-chromosome SNP Calls with Yleaf v. 2.3 from FASTQ files, bwa-mem with hg38 reference, and parameters r=1, q=0, b=0.

Google Drive.

Haplogroup.info.

The following is a list of automated Y-DNA haplogroup predictions obtained with Clean tree v2:

WARNING: Please note that the haplogroup prediction algorithm works best with modern DNA, and its strict requirements make the prediction rather impractical for ancient DNA – in fact, males usually turn out to have not enough quality for a reliable prediction.
If anything, positive haplogroup predictions (especially under R1b and I2) will normally turn out to be wrong because they are based on few reads, due to the sample being either a) female or b) low coverage.

The usual process for checking out Y-chromosome haplogroups in ancient DNA samples is as follows:

Select the male individual you want to check out for in the Ancient DNA Dataset.

Look up its library ID (object-ID) at ENA Browser search form (top right) to obtain the accession number(s) for the available sample(s) corresponding to that individual.

Look for files obtained with Yleaf for that accession number(s); more specifically, look for individual Derived and Ancestral SNPs in the ACCESSION_NUMBER.out or ACCESSION_NUMBER.out.csv documents.
When in doubt about a specific sample, you can ask a question in this thread.
```
ERR4896481 R1b1a1b R-CTS1416^^/etc*(xYSC0000054,L884.2,Y10790,Y7369,S22641,L356,L564,AM01878) 503105 425 1.0 1.0 1.0 1.0
ERR4896466 NA NA 3155825 15449 0.0 0.0 1.0 0.0
ERR4896497 R1b1a1b1a1 R-CTS7650*(xL276,FGC11355) 257899 318 1.0 1.0 1.0 1.0
ERR4896499 NA NA 168097 220 0 0 0 0
ERR4896448 NA NA 2500695 11607 0.0 0.0 1.0 1.0
ERR4896496 Q1a1b Q-Z36013/etc*(xZ36049) 2728514 11373 1.0 1.0 1.0 1.0
ERR4896443 NA NA 936381 945 0 0 0 0
ERR4896467 NA NA 2763178 12330 0 0 0 0
ERR4896461 NA NA 2806702 14034 0.0 0.0 1.0 0.0
ERR4896508 NA NA 2160338 7895 0.0 0.0 1.0 1.0
ERR4896468 NA NA 1266990 6466 0 0 0 0
ERR4896459 NA NA 3187654 15143 0.0 0.0 1.0 0.0
ERR4896487 NA NA 540827 392 0 0 0 0
ERR4896493 NA NA 2632653 11094 0.0 0.0 1.0 0.0
ERR4896491 NA NA 17203 18 0 0 0 0
ERR4896454 NA NA 94358 171 0 0 0 0
ERR4896439 NA NA 2965465 15046 0.0 0.0 1.0 0.0
ERR4896447 R1a R-L145/etc*(xY177,YP4149) 2775051 11847 1.0 1.0 1.0 1.0
ERR4896457 R1b R-CTS46*(xFGC17520,BY3323,Y7369,S1746,S22641,L276,L165,L356,L564,A5845,BY15390,Y24710,BY14575) 569255 645 1.0 1.0 1.0 1.0
ERR4896458 R1b1a1b R-PF6504/etc*(xYSC0000054,S18461,S379,FGC396,L1231,FGC5007,FGC19851,FGC5606,A11313,Z17836,A6464,L1308,FGC5782,FGC33060,L1315,CTS300,AM01878) 746711 753 1.0 1.0 1.0 1.0
ERR4896435 NA NA 3608752 16187 0.0 0.0 1.0 0.0
ERR4896475 NA NA 873821 837 0.0 0.0 1.0 1.0
ERR4896440 NA NA 1875378 8531 0.0 0.0 1.0 0.0
ERR4896488 NA NA 868627 1018 0.0 0.0 1.0 1.0
ERR4896449 NA NA 65993 138 0 0 0 0
ERR4896501 Q1b1 Q-L475/etc*(xM194,CTS748^,Z5917,M720,Z19486,Z19316,Z19366,Z19433,SK281,CTS2731,Z35571,Z35744,Z35749,BZ3493,BZ2090,Y18715,FGC8462,BY1052,M944,L334,YP4070) 2463499 8496 1.0 1.0 1.0 1.0
ERR4896480 NA NA 17390 13 0 0 0 0
ERR4896452 NA NA 82631 142 0 0 0 0
ERR4896500 NA NA 234598 230 0 0 0 0
ERR4896495 Q1a1b Q-YP1500/etc 1181883 4694 1.0 1.0 1.0 1.0
ERR4896441 NA NA 164578 187 0 0 0 0
ERR4896437 NA NA 2448464 11789 0 0 0 0
ERR4896460 NA NA 722926 3115 0.0 1.0 1.0 0.0
ERR4896503 NA NA 1841502 5657 0 0 0 0
ERR4896473 NA NA 2109227 8051 0 0 0 0
ERR4896484 NA NA 2114007 7092 0.0 0.0 1.0 1.0
ERR4896485 NA NA 388080 359 0 0 0 0
ERR4896436 NA NA 1888067 7056 0.0 0.0 1.0 0.0
ERR4896450 NA NA 202478 248 0 0 0 0
ERR4896462 R1b1a1b R-PF6462*(xFGC36479,L1231,L356,L564) 820294 836 1.0 1.0 1.0 1.0
ERR4896486 NA NA 142071 132 0 0 0 0
ERR4896476 NA NA 591387 451 0 0 0 0
ERR4896470 NA NA 530538 457 0 0 0 0
ERR4896469 NA NA 601602 481 0 0 0 0
ERR4896504 Q1a Q-F5087*(xF4974,Y9310) 1255159 3966 1.0 1.0 1.0 1.0
ERR4896506 NA NA 1319548 4226 0 0 0 0
ERR4896438 NA NA 1471162 5124 0.0 0.0 1.0 1.0
ERR4896463 R1b1a1b R-CTS1416^^/etc*(xPF7595,BY281,BY1734.1,FGC5627,FGC5782) 115660 208 1.0 1.0 1.0 1.0
ERR4896507 R1a~ R-F1769/etc*(xCTS11853,YP5018,Y18467) 1647977 4205 1.0 1.0 1.0 1.0
ERR4896498 Q1a1b Q-Z36019/etc*(xZ43867,Z36044) 3790695 16691 1.0 1.0 1.0 1.0
ERR4896472 R1b1a1b1a1a R-L11/etc*(xFGC17470,FGC14877,YSC0000054,AMM490.2,BY1053,FGC6184,FGC15335,BY97502,FGC33321,S20039,Z348,S12025,L221,A8056) 1030684 3422 1.0 1.0 1.0 1.0
ERR4896502 NA NA 2377223 8631 0.0 0.0 1.0 1.0
ERR4896451 NA NA 167891 238 0 0 0 0
```
January 20, 2021 at 11:20 am #35222
Carlos Quiles
Keymaster
Y-SNP calls for males only obtained with YLeaf v.2.2 + automatic haplogroup inference with pathPhynder v.1, both using FTDNA’s Haplotree standard for clarity. Colored HTML and simple CSV version of the files included for easy reference.

NOTE. To avoid the extreme overhead of web crawlers, only limited access is provided for anonymous users. To request full access you will need to be registered in this forum, and to show a minimum (real or online) background, here or elsewhere. Preferable experience with SNP calls, such as FTDNA or YFull group administrators, including frequent participants and the like. Contact [email protected] with details. I will not answer emails from anonymous users with no details.
To request just a specific set of ancestral and derived SNPs for one or more samples, ask in the appropriate thread instead.

I20769 / 1240K:

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20761 / 1240K: Q>MEH2>M346>L53>YP3961;Q>MEH2>M346>L53>YP3961>YP3955;Q>MEH2>M346>L53>YP3961>YP3955>YP3953;C>M217>F1067>CTS10762;Q>MEH2>M346>L53>YP3961>YP3955>YP3953>YP4024;I1>DF29>Y2592>CTS6364>CTS10028>S6346>L22>Z2338>L205>A1463>FT121995>A1465>Y51401>FT304967

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20757 / 1240K: Q>MEH2>F1096>F1202>NGQ11>B143;A00;Q>MEH2>M346>Y4800>SK1932>Z36057>BY62534

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11906 / 1240K: H

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11917 / 1240K: F;A00

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20778 / 1240K: Q>MEH2>F1096>F1202>NGQ11>B143>Z36017;J>M267>CTS12238>PH77>PF7261>PF7257>FT27095>PH7

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20756 / 1240K: Q>MEH2>F1096>F1202>NGQ11>B143;A00;Q>MEH2>M346>Y4800>SK1932>Z36057>BY62534

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11926 / 1240K: N;G>L89>P15>L1259>L30>L141>P303>L140>PF3346>PF3345>L497>CTS9737>Z1817>Z727>CTS2230>Z726>CTS4803>S2808>BY46757>S23438>S18765>FT7941>Z41143>FT39559>L667

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11920 / 1240K: R1b

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11908 / 1240K: F;A00

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11904 / 1240K: I2>CTS2257>L596

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11934 / 1240K: I2>CTS2257>L596

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20767 / 1240K:

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11928 / 1240K: N;G>L89>P15>L1259>L30>L141>P303>L140>PF3346>PF3345>L497>CTS9737>Z1817>Z727>CTS2230>Z726>CTS4803>S2808>BY46757>S23438>S18765>FT7941>Z41143>FT39559>L667

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11903 / 1240K: I2;I2>CTS2257;E>CTS9083>P147>M132>Z965>CTS230>CTS9548>Z5985.1>Z36224

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20760 / 1240K: Q>MEH2>F1096>M25;Q>MEH2>F1096>M25>L712;R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>Z290>L21>DF13>Z39589>S1051>FGC9826;B>CTS1388>M182

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20754 / 1240K:

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20759 / 1240K: Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276>Y4303>Z35703;R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>ZZ11>U152>Z36>FGC6472>BY85509>FT233826;Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276>Y4303;Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11915 / 1240K: R1a>M459>M198>M417>PF6162>Z93

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11921 / 1240K: R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>Z290>L21>DF13>ZZ10_1>Z253>FGC3268>ZZ6_1>FGC3220>FGC3222>Z17692;BT

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11916 / 1240K: R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>Z290>L21>DF13>ZZ10_1>Z253>FGC3268>ZZ6_1>FGC3220>FGC3222>Z17692;BT

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11914 / 1240K: R1a>M459>M198>M417>PF6162>Z93

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20772 / 1240K: R1a>M459>M198>M417>PF6162>Z283>Z282;R1a>M459>M198>M417>PF6162>Z283

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11933 / 1240K: I2>CTS2257>L596

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20777 / 1240K: C>M217>F1906>F3447>F6301>FGC16273>F3918>F11350>F17066

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20750 / 1240K: R1a>M459>M198;R1a>M459;R1a;R1a>M459>M198>M417;G>L89>P15>L1259>L30>M406>PF3299>PF3293>PF3296>Z30814>Z30797>Z30793>FT75972>BY68816;D>M174>CTS11577>F6251>M15>PH4

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20766 / 1240K: R1b>L754>L389>P297>M269>L23>L51>P310;R1b>L754>L389>P297>M269>L23>L51>P310>L151

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11902 / 1240K: I2>CTS2257>L596

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11907 / 1240K: H

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20745 / 1240K: I1;I>M170>Z2699;A0

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20782 / 1240K: Q>MEH2>F1096>M25;Q>MEH2>F1096>M25>L712;R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>Z290>L21>DF13>Z39589>S1051>FGC9826;B>CTS1388>M182

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20784 / 1240K:

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20783 / 1240K: Q>MEH2>M346>L53>YP3961;Q>MEH2>M346>L53>YP3961>YP3955;Q>MEH2>M346>L53>YP3961>YP3955>YP3953;C>M217>F1067>CTS10762;Q>MEH2>M346>L53>YP3961>YP3955>YP3953>YP4024;I1>DF29>Y2592>CTS6364>CTS10028>S6346>L22>Z2338>L205>A1463>FT121995>A1465>Y51401>FT304967

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11935 / 1240K: I2>CTS2257>L596

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11919 / 1240K: R1b>L754

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20762 / 1240K: R1a>M459>M198;R1a>M459;R1a;R1a>M459>M198>M417;G>L89>P15>L1259>L30>M406>PF3299>PF3293>PF3296>Z30814>Z30797>Z30793>FT75972>BY68816;D>M174>CTS11577>F6251>M15>PH4

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20744 / 1240K: R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11927 / 1240K: N>B482;G>L89>P15>L1259>L30>L141>P303>L140>PF3346>PF3345>L497>CTS9737>Z1817>Z727>CTS2230>Z726>CTS4803>Z6150>FT287125>FT6731

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20755 / 1240K: C>M217>F1906>F3447>F6301>FGC16273>F3918>F11350>F17066

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11913 / 1240K: R1a>M459>M198;R1a>M459;R1a;R1a>M459>M198>M417;G>L89>P15>L1259>L30>M406>PF3299>PF3293>PF3296>Z30814>Z30797>Z30793>FT75972>BY68816;D>M174>CTS11577>F6251>M15>PH4

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20781 / 1240K: Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276>Y4303>Z35703;R1b>L754>L389>P297>M269>L23>L51>P310>L151>P312>ZZ11>U152>Z36>FGC6472>BY85509>FT233826;Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276>Y4303;Q>MEH2>M346>L53>L54>CTS3814>CTS11969>M3>Y4276

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I11918 / 1240K: F;A00

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.

I20779 / 1240K: Q>MEH2>F1096>F1202>NGQ11>B143;A00;Q>MEH2>M346>Y4800>SK1932>Z36057>BY62534

Y-SNP CALLS: Only derived calls or all SNP calls (slow to load!)

pathPhynder files: Best Path • Best Path (Tree) • All Counts • Best Node • All Paths.

YLeaf v.2.2 files: SNPs • SNPs (CSV) • Derived SNPs • Derived SNPs (CSV) • FMF • CHR • LOG.
Author

Posts

Viewing 2 posts - 1 through 2 (of 2 total)

You must be logged in to reply to this topic.