BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525096.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 = 761,475 number of mapped reads = 702,095 (92.2%) number of supplementary alignments = 3,067 (0.4%) number of secondary alignments = 0 number of mapped bases = 40,929,473 bp number of sequenced bases = 40,916,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,927 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1254 >>>>>>> ACTG content number of A's = 9,940,850 bp (24.3%) number of C's = 7,481,411 bp (18.28%) number of T's = 13,330,852 bp (32.58%) number of G's = 10,162,064 bp (24.84%) number of N's = 845 bp (0%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 202,439 number of insertions = 2,457 mapped reads with insertion percentage = 0.35% number of deletions = 8,426 mapped reads with deletion percentage = 1.19% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 0.1577X There is a 1.25% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 4551957 0.018262570346815707 0.2585813761032037 chr2 243199373 3515848 0.014456649113153757 0.1853473729206128 chr3 198022430 2850929 0.014397000380209454 0.12617741688689846 chr4 191154276 1838552 0.009618157848585088 0.10445649897990208 chr5 180915260 1970422 0.010891408496994671 0.10847513556998062 chr6 171115067 2648998 0.015480799244873042 0.13849863379005747 chr7 159138663 2972865 0.0186809725804973 0.2656922902516391 chr8 146364022 2114973 0.014450088014115929 0.14318914156923093 chr9 141213431 1406421 0.009959541313035586 0.11933803825360305 chr10 135534747 2261979 0.01668929222998439 0.18229871816965118 chr11 135006516 1927011 0.01427346662289989 0.139468983023894 chr12 133851895 1930694 0.014424106584370733 0.12516611525412816 chr13 115169878 955897 0.00829988723266686 0.09511257139419635 chr14 107349540 1570530 0.014630058032852307 0.12650143706439484 chr15 102531392 816053 0.007959055115529886 0.09407841808571933 chr16 90354753 1094702 0.012115599497018159 0.11973229944652015 chr17 81195210 719583 0.008862382399158769 0.10010745905341392 chr18 78077248 911549 0.011674963236409153 0.1971521600948126 chr19 59128983 669613 0.011324615544292382 0.18601685702734694 chr20 63025520 737827 0.011706797500441091 0.11323472297702256 chr21 48129895 544799 0.011319347361967026 0.1140893575850777 chr22 51304566 469740 0.009155910216646215 0.0991374527300931 chrMT 16571 2874 0.17343551988413494 0.42884544213876835 chrX 155270560 2335307 0.015040243301756625 0.13308529311929918 chrY 59373566 110350 0.0018585712032186175 0.05989215512925759