LAPMO Université de Provence – URA 164 CNRS/AFAN.
Inner ring: GC content from low (brown, <30%) to high (orange, >55%). Outer concentric rings: from inner to outer, coverage plots of OBS107, 110, 116, 124, and 137 on a logarithmic scale. Axes are …
(A) Maximum likelihood phylogeny of Y. pestis genomic SNPs showing the position of the Observance (OBS) lineage (red) relative to those of 130 modern (black) and three ancient strains (Black Death …
Quantitative PCR data for the pla gene obtained for the 19 Observance teeth extracted. Values below std curve detection are highlighted in grey.
PCR Blks: | Copies per μl |
---|---|
PCR Blk 1 | 0 |
PCR Blk 2 | 0 |
PCR Blk 3 | 0 |
PCR Blk 4 | 0 |
Extraction Blks: | Copies per μl |
BLk 1 | 0 |
Blk 2 | 0 |
Blk 3 | 0 |
Blk 4 | 0 |
Extracts: | |
Sample | Copies per μl |
101a | 0 |
101b | 0 |
102 | 0 |
103 | 0 |
107 | 39 |
108 | 0 |
109 | 0 |
110 | 50 |
116 | 105 |
117a | 0 |
117b | 1 |
118 | 0 |
123 | 0 |
124 | 142 |
125 | 0 |
126 | 0 |
130 | 0 |
134 | 1 |
137 | 30 |
144 | 0 |
Mapping statistics.
Sample ID | Raw read pairs | Preprocessed reads | Mapped reads | % mapped | Dedupped | Duplication factor | Fold coverage | % covered |
---|---|---|---|---|---|---|---|---|
OBS107 | 14,646,710 | 15,395,287 | 1,850,734 | 12.02% | 851,096 | 2.17 | 12.20 | 84.79 |
OBS110 | 9,879,257 | 10,458,571 | 1,581,158 | 15.12% | 855,988 | 1.85 | 14.61 | 90.63 |
OBS116 | 16,858,273 | 17,876,883 | 2,931,554 | 16.40% | 1,363,415 | 2.15 | 20.04 | 92.56 |
OBS124 | 48,797,602 | 52,345,884 | 4,972,347 | 9.50% | 973,763 | 5.11 | 13.34 | 85.37 |
OBS137 | 120,018,142 | 129,095,434 | 12,669,625 | 9.81% | 1,583,596 | 8.00 | 24.40 | 92.76 |
Combined SNP table from three SNP calling approaches.
List of genomes used in SNP calling and phylogeny.