The 0.3% of DNA does not replicate during the S phase. This DNA replication occurs in

Solution(By Examveda Team)

The 0.3% of DNA does not replicate during the S phase. This DNA replication occurs in Zygotene.
S phase (Synthesis Phase) is the phase of the cell cycle in which DNA is replicated, occurring between G₁ phase and G₂ phase. Since accurate duplication of the genome is critical to successful cell division, the processes that occur during S-phase are tightly regulated and widely conserved.
Zygotene is the second stage of meiosis prophase-1 after the S phase, here uncoiling and condensing of chromosomes takes place. Also, the leftover DNA that does not replicate during S-phase, replicates in the zygotene phase.