BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524717.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 = 567,177 number of mapped reads = 516,008 (90.98%) number of supplementary alignments = 1,579 (0.28%) number of secondary alignments = 0 number of mapped bases = 29,856,079 bp number of sequenced bases = 29,846,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,100 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4753 >>>>>>> ACTG content number of A's = 7,198,831 bp (24.12%) number of C's = 5,698,007 bp (19.09%) number of T's = 9,984,963 bp (33.45%) number of G's = 6,961,366 bp (23.32%) number of N's = 3,806 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 154,108 number of insertions = 2,420 mapped reads with insertion percentage = 0.47% number of deletions = 5,690 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.21% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1265X There is a 0.92% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2392618 0.009599245893152659 0.19459712553350186 chr2 243199373 2541884 0.010451852604077232 0.16756697968795342 chr3 198022430 1997385 0.010086660384886701 0.10356083590937665 chr4 191154276 1940080 0.010149289048600723 0.1081433767808765 chr5 180915260 1830613 0.010118621281587855 0.10373391182549617 chr6 171115067 1725428 0.010083437012592233 0.11052069276311853 chr7 159138663 1647307 0.010351393991540572 0.14366175645458343 chr8 146364022 1505553 0.010286359854199689 0.12904598644743717 chr9 141213431 1244156 0.00881046506121645 0.10975074524209835 chr10 135534747 1483315 0.010944167697453997 0.13474574723512156 chr11 135006516 1349013 0.00999220659838374 0.1145468405138849 chr12 133851895 1340627 0.010015749123312748 0.10421428411625593 chr13 115169878 936331 0.008129999061039207 0.09365221982426802 chr14 107349540 896798 0.008353999467533815 0.09557080142405672 chr15 102531392 839710 0.008189784451575572 0.09324019224860029 chr16 90354753 860947 0.009528519213593555 0.1057761083599897 chr17 81195210 786820 0.009690473120273968 0.10330043841555656 chr18 78077248 807398 0.010341015093154923 0.15111792284892062 chr19 59128983 626281 0.010591776963253368 0.1597819413740717 chr20 63025520 603443 0.00957458185192284 0.10163044069256266 chr21 48129895 402673 0.008366380188446286 0.10067259375609726 chr22 51304566 350061 0.006823193865434901 0.0848893229025642 chrMT 16571 3317 0.20016896988715224 0.45512124625368644 chrX 155270560 1645531 0.010597830007182302 0.10973368909800524 chrY 59373566 98790 0.0016638717640776368 0.07615696252549188