Ancient DNA Analysis

PCA Visualization

• Interactive PCA Visualization - 3D visualization of PCA results for both Chachapoya and Nazca samples

Static PCA Plots

Nazca PCA

• PC1 vs PC2 Plot (PDF)
• PC2 vs PC3 Plot (PNG)
• PC1 vs PC3 Plot (PDF)

Chachapoya PCA

• PC1 vs PC2 Plot (PDF)
• PC2 vs PC3 Plot (PNG)
• PC1 vs PC3 Plot (PDF)

Nazca Analysis

nf-core/eager Reports

• hg38 momia1, momia3, momia5, momia6 nf-core/eager MultiQC Report
• hg38 ancient0002, ancient0003, ancient0004 nf-core/eager MultiQC Report

Chachapoya Analysis

Sample Information

• Sample NA50 was obtained from a dataset of pre-Columbian Chachapoyan and Chachapoya-Inca remains dating between 1000 and 1500 AD
• Location: Laguna de los Condores, northeastern Peru
• Material: Bone samples

Sequence Data

• Precapture NA50
• Postcapture NA50

nf-core/eager Reports

• Precapture NA50 nf-core/eager MultiQC Report - Damage patterns for precapture data
• Postcapture NA39-50 nf-core/eager MultiQC Report - Damage patterns for postcapture data

Mitochondrial DNA Analysis (rCRS)

nf-core/eager Reports

• rCRS momia1, momia3, momia5, momia6 nf-core/eager MultiQC Report
• rCRS ancient0002, ancient0003, ancient0004 nf-core/eager MultiQC Report

Nazca Samples Analysis

Sample	SRA Accession	Consensus Sequence	Haplogroup
ancient0002	SRR21031366	Download FASTA	H27
ancient0003	SRR20755928	Download FASTA	M20
ancient0004	SRR20458000	Download FASTA	M20*

Haplogroup Results	Haplogroup Summary

Nazca Sample Overview

Nuclear Genome Statistics (hg38 Reference)

Sample	Individual	Total Reads	Mapped Reads (%)	Mean Coverage	C14 Dating
ancient0002	Victoria	561,665,320	76.9M (13.4%)	0.9X	~790 +/- 30 YBP (UNAM), ~1040 YBP (LAC-UFF)
ancient0003	Maria	647,789,366	741.2M (95.4%)	15.1X	~1750 +/-30 YBP (Beta Analytics)
ancient0004	Victoria	501,700,245	66.5M (13.0%)	0.6X	~790 +/- 30 YBP (UNAM), ~1040 YBP (LAC-UFF)

Mitochondrial Genome Statistics (rCRS Reference)

Sample	Individual	Total Reads	Mapped Reads	mtDNA Haplogroup
ancient0002	Victoria	561,665,320	7,408	H27
ancient0003	Maria	647,789,366	64,090	M20
ancient0004	Victoria	501,700,245	17,111	M20*

All samples date to the pre-European contact period. Maria (ancient0003) shows excellent genome coverage at 15.1X with very high endogenous DNA content (95.4%). The Victoria samples (ancient0002, ancient0004) show lower coverage and endogenous DNA content (~13%), but still yielded sequences.

Y-Chromosome Haplogroup Analysis (hg38 Reference)

Sample	Individual	Y-Haplogroup	QC Score	Valid Markers	Details
ancient0002	Victoria	No call	-	-	Insufficient Y-chr coverage
ancient0003	Maria	Q-Z770	1.0	128	View Analysis
ancient0004	Victoria	No call	-	-	Insufficient Y-chr coverage

Maria's Y-chromosome was assigned to haplogroup Q-Z770 with high confidence (QC score: 1.0) based on only 128 valid markers. Detailed analysis files:

• Haplogroup Prediction
• Filtered Marker Analysis
• Analysis Log

Chachapoya Samples Analysis

Sample	SRA Accession	Consensus Sequence	Haplogroup
NA39	SRR1313909	Download FASTA	B2
NA40	SRR1314212	Download FASTA	R
NA41	SRR1314213	Download FASTA	L3
NA43	SRR1314599	Download FASTA	R
NA47	SRR1314600	Download FASTA	R
NA50	SRR1314601	Download FASTA	R

Haplogroup Results	Haplogroup Summary

Detailed Results and Analysis Files

• View Haplogrep3 Haplogroup Analysis Report (Nazca)
• Download Complete Haplogrep3 Analysis Files (Nazca)
• View Haplogrep3 Haplogroup Analysis Report (Chachapoya)
• Download Complete Haplogrep3 Analysis Files (Chachapoya)