(A) DNA damage patterns for RISE505 and RISE509. The frequencies of all possible mismatches observed between the Y. pestis CO92 chromosome and the reads are reported in gray as a function of distance from 5′ (left panel, first 25 nucleotides sequenced) and distance to 3′ (right panel, last 25 nucleotides). The typical DNA damage mutations C>T (5′) and G>A (3′) are reported in red and blue, respectively.

(B) Ancient DNA damage patterns (n = 7) of the reads aligned to the CO92 chromosome and the Y. pestis associated plasmids pMT1, pCD1 and pPCP1. The boxplots show the distribution of C-T damage in the 5′ of the reads. The lower and upper hinges of the boxes correspond to the 25th and 75th percentiles, the whiskers represent the 1.5 inter-quartile range (IQR) extending from the hinges, and the dots represent outliers from these.

(C) DNA fragment length distributions from RISE505 and RISE509 samples representing both the Y. pestis DNA and the DNA of the human host. The declining part of the distributions is fitted to an exponential model (red).

(D) Linear correlation (red) between the decay constant in the DNA of the human host and the associated Y. pestis DNA extracted from the same individual (R2 = 0.55, p = 0.055). The decay constant (λ) describes the damage fraction (i.e., the fraction of broken bonds on the DNA strand).

(E) Distribution of edit distance of high quality reads from RISE505 and RISE509 samples mapped to either Y. pestis (dark gray) or Y. pseudotuberculosis (light gray) reference genomes. The reads have a higher affinity to Y. pestis than to Y. pseudotuberculosis.