Q: Why are some journals in the Clarivate Analytics Master List not a part of the JCR list?
Jordan Journal of Biological Science and Baghdad Science Journal are both there in the Master List but I cannot find them in JCR list. Are those journals under Web of Science? Are the journals in the Master List covered by ISI if can't find them in JCR reports?
All journals in the Clarivate Analytics Master List are included in the Web of Science, that is, they are all ISI indexed. However, only the ones in the Journal Citation Reports (JCR) have an impact factor. So probably the two journals that you mentioned are ISI indexed but do not have impact factors which is why they don't appear on the JCR list.
The Web of Science Core Collection includes several indexes (SCIE, SSCI, AHCI, ESCI, Book Citation Index and Conference Proceedings Citation Index). Only the first two (Science Citation Index Expanded and Social Sciences Citation Index) get passed to the Journal Citation Reports and have metrics such as the Journal Impact Factor.