重测序BWA比对率低

老师您好，请问做BWA比对时与参考基因组的比对率很低，已经确定过与参考基因组为同一物种，是因为污染太严重吗，这样会对后续分析有影响吗？

38280780 + 0 primary

616640 + 0 secondary

0 + 0 supplementary

4716288 + 0 duplicates

4716288 + 0 primary duplicates

20943404 + 0 mapped (53.84% : N/A)

20326764 + 0 primary mapped (53.10% : N/A)

38280780 + 0 paired in sequencing

19140390 + 0 read1

19140390 + 0 read2

17205178 + 0 properly paired (44.94% : N/A)

18888798 + 0 with itself and mate mapped

1437966 + 0 singletons (3.76% : N/A)

1344176 + 0 with mate mapped to a different chr

923040 + 0 with mate mapped to a different chr (mapQ>=5)

36840465 + 0 in total (QC-passed reads + QC-failed reads)

36592656 + 0 primary

247809 + 0 secondary

0 + 0 supplementary

1589678 + 0 duplicates

1589678 + 0 primary duplicates

7913971 + 0 mapped (21.48% : N/A)

7666162 + 0 primary mapped (20.95% : N/A)

36592656 + 0 paired in sequencing

18296328 + 0 read1

18296328 + 0 read2

5977810 + 0 properly paired (16.34% : N/A)

6399802 + 0 with itself and mate mapped

1266360 + 0 singletons (3.46% : N/A)

352116 + 0 with mate mapped to a different chr

243973 + 0 with mate mapped to a different chr (mapQ>=5)

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