I have a few resequencing data (Illumina DNA Seq) for various cultivars/varieties of same plant.

I had mapped the reads with a published contig level assembled genome and got high mapping percentage (81-95%). Now I have a new chromosome level genome assembly (same variety), but mapping the resequenced files to this genome gives very low mapping percentage (46-58%).

Any idea why this is happening and what may have gone wrong.

The mapping stats are as below for one sample.

With Old Reference Genome:

145054599 + 0 in total (QC-passed reads + QC-failed reads)
1611499 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
142412496 + 0 mapped (98.18% : N/A)
143443100 + 0 paired in sequencing
71721550 + 0 read1
71721550 + 0 read2
131411528 + 0 properly paired (91.61% : N/A)
139931536 + 0 with itself and mate mapped
869461 + 0 singletons (0.61% : N/A)
7957102 + 0 with mate mapped to a different chr
3840456 + 0 with mate mapped to a different chr (mapQ>=5)

With New Reference

146109857 + 0 in total (QC-passed reads + QC-failed reads)
2666757 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
81681317 + 0 mapped (55.90% : N/A)
143443100 + 0 paired in sequencing
71721550 + 0 read1
71721550 + 0 read2
60751250 + 0 properly paired (42.35% : N/A)
66110132 + 0 with itself and mate mapped
12904428 + 0 singletons (9.00% : N/A)
4092218 + 0 with mate mapped to a different chr
3161215 + 0 with mate mapped to a different chr (mapQ>=5)