BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716494.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,385,870 number of mapped reads = 1,222,495 (88.21%) number of supplementary alignments = 5,546 (0.4%) number of secondary alignments = 0 number of mapped bases = 70,056,310 bp number of sequenced bases = 70,036,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,426 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.341 >>>>>>> ACTG content number of A's = 17,937,495 bp (25.61%) number of C's = 12,873,851 bp (18.38%) number of T's = 22,724,112 bp (32.45%) number of G's = 16,499,321 bp (23.56%) number of N's = 1,898 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 351,763 number of insertions = 5,270 mapped reads with insertion percentage = 0.43% number of deletions = 12,895 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.62% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2499X There is a 2.06% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7555968 0.030314740920946392 0.5235600275335246 chr2 243199373 4006116 0.016472558915684377 0.2789230861626674 chr3 198022430 5040659 0.02545499012409857 0.1722495706022414 chr4 191154276 3433064 0.01795965055994876 0.14993942266704238 chr5 180915260 4633940 0.025613870272745372 0.17361721038178426 chr6 171115067 5130372 0.029982000357689133 0.20812819371929422 chr7 159138663 5499190 0.03455596456783101 0.3649725155280277 chr8 146364022 4407453 0.030112953578168275 0.21109870054096147 chr9 141213431 3065482 0.021708147576982247 0.1962870887563756 chr10 135534747 3805246 0.028075796681127092 0.24121230279264647 chr11 135006516 2424960 0.017961799710467307 0.17930432715035094 chr12 133851895 2988650 0.022328036521261054 0.16414758373018729 chr13 115169878 1704830 0.014802742085044146 0.13180722500998246 chr14 107349540 1689520 0.01573849315050628 0.140625092149076 chr15 102531392 1523903 0.014862794411296006 0.13218415878134762 chr16 90354753 1550978 0.01716542792165012 0.1534037198697314 chr17 81195210 969897 0.01194524898697842 0.1211245054271492 chr18 78077248 2008908 0.02572974908132008 0.3147470221853486 chr19 59128983 1829586 0.030942287642593144 0.34184214332851054 chr20 63025520 635632 0.010085311473828379 0.11094203584533044 chr21 48129895 913465 0.018979160457341535 0.1556693592886838 chr22 51304566 878764 0.017128378008304367 0.14026993286986908 chrMT 16571 108646 6.556393699837065 3.9974308048884013 chrX 155270560 4085870 0.02631451834784392 0.1935773480463184 chrY 59373566 165211 0.0027825682560484915 0.07507421915066545