BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716626.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 = 1,246,863 number of mapped reads = 1,132,635 (90.84%) number of supplementary alignments = 4,545 (0.36%) number of secondary alignments = 0 number of mapped bases = 64,816,632 bp number of sequenced bases = 64,799,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,269 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5876 >>>>>>> ACTG content number of A's = 16,809,147 bp (25.94%) number of C's = 12,434,104 bp (19.19%) number of T's = 19,387,497 bp (29.92%) number of G's = 16,166,778 bp (24.95%) number of N's = 1,532 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 316,477 number of insertions = 4,880 mapped reads with insertion percentage = 0.43% number of deletions = 10,481 mapped reads with deletion percentage = 0.92% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.1922X There is a 1.93% of reference with a coverageData >= 1X There is a 0.12% 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 5320127 0.021344488445627585 0.29192674171661914 chr2 243199373 5565228 0.02288339781204946 0.217772799645272 chr3 198022430 4341234 0.02192294074969184 0.15738184757461207 chr4 191154276 4166779 0.02179799001723613 0.1662192920045009 chr5 180915260 3914202 0.021635554679024865 0.15800631388178268 chr6 171115067 3729738 0.02179666621642383 0.16539575080590943 chr7 159138663 3567941 0.022420327862123612 0.2122008124800191 chr8 146364022 3323316 0.022705825889370545 0.17995995894183764 chr9 141213431 2788561 0.019747137225211955 0.1996518558056626 chr10 135534747 3082768 0.022745222669726162 0.18509535937546626 chr11 135006516 2954308 0.02188270675765013 0.1935537264592093 chr12 133851895 2918921 0.021807095073252417 0.15917252413299082 chr13 115169878 2011493 0.017465443525085615 0.13990464667283334 chr14 107349540 1998395 0.018615776089958094 0.1510096179533335 chr15 102531392 1909774 0.01862623692849113 0.14509748793165728 chr16 90354753 1500854 0.016610681233338108 0.14656780124317184 chr17 81195210 1633103 0.02011329239742098 0.15648634435344183 chr18 78077248 1740369 0.02229034763110503 0.33771628503855217 chr19 59128983 1332399 0.022533771636153457 0.21325846254154748 chr20 63025520 1421801 0.022559131602563533 0.16331651928879462 chr21 48129895 872338 0.018124660359221643 0.1551692006893107 chr22 51304566 824747 0.016075508756861912 0.13474707705871194 chrMT 16571 2715 0.16384044414941765 0.4170476503120002 chrX 155270560 3709182 0.023888507905168888 0.18032201048587035 chrY 59373566 186339 0.00313841685035391 0.07866011263596875