Geographic location of the samples from which ancient HBV genomes were isolated. Radiocarbon dates of the specimens is given in two sigma range. Icons indicate the sample material (tooth or mummy). …
References shown in Supplementary file 1 were used to carry out the alignment.
([M + 2 hr]2+): m/z = 1237.6429 Da. Mass accuracy of the precursor peptide = 0.56 ppm.
Network of 493 modern, two published ancient genomes (light yellow box), and three ancient hepatitis B virus (HBV) obtained in this study (grey box). Colors indicate the eight human HBV genotypes (A–…
Results of the recombination analysis using the methods RDP, GENECOV, Chimera, MaxChi, BootScan, SiScan, 3Seq within the RDP v4 software package with all modern full reference genomes (n = 493) and five ancient genomes.
Multiple sequence alignment of the 493 representative and five ancient HBV genomes.
The multiple sequence alignment was stripped of any sites that had gaps in more than 95%.
Maximum-likelihood tree based on the multiple sequence alignment of the 493 representative and five ancient HBV genomes with 2000 replicates.
Neighbour-Joining tree based on the multiple sequence alignment of the 493 representative modern and five ancient HBV genomes with 10000 replicates.
Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the …
Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the …
Organization of overlapping open reading frames and approximate location of single-stranded portion of plus strand are indicated. Gaps in the sequence are marked in red. The green plot depicts the …
Gaps or non-called sites (’N') were ignored.
In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups of (a) the eight human genotypes, two primate genotypes, and four …
In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups or 50% consensus sequences of (a) the eight human genotypes, two …
In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups or 50% consensus sequences of (a) the eight human genotypes, two …
In each case, sequence fragments of 200 bases incrementing by 20 bases, 100 bootstrap replicates, were compared with sequence groups of the eight human genotypes, four primate genotypes and four …
Each dot represents one sample.
*Merged reads | Length of HBV consensus sequence | Mean HBV coverage | Gaps in the consensus sequence at nt position | *Mapped reads HBV | *Mapped reads human | Mean human coverage | Human genomes/HBVgenomes | |
---|---|---|---|---|---|---|---|---|
Karsdorf | 386,780,892 | 3183 | 104X | 2157–2175; 3107–3128; 3133–3183 | 10,718 | 122,568,310 | 2.96X | 1: 35.1 |
Sorsum | 367,574,767 | 3182 | 47X | - | 3249 | 9,856,001 | 1.17X | 1: 40.2 |
Petersberg | 419,413,082 | 3161 | 46X | 880–1000; 1232–1329; 1331–1415; 1420–1581; 1585–1598 | 2125 | 105,476,677 | 2.88X | 1: 16 |
*number.
nt, nucleotide.
Accession numbers for the reference genomes used in the first alignment step to catch HBV diversity in the sample.
Since monkey HBV strains are not classified into genotypes the column is left blank.
Number of reads mapping against the references shown in Supplementary file 1 before and after duplicate removal.
Number of contigs and combined contig length of the de novo assembly for chosen K-values.
Final consensus length after retrieving gap information from the multiple sequence alignment with Geneious.
Number of reads mapping against hg19 before and after duplicate removal and percentage of the genome where coverage is at least one.
Basic statistics for the mapping against the references shown in table S1.
Shown are mean coverage, mean coverage for the covered region, genome length, number of missing bases and covered bases