BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717028.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 = 2,787,177 number of mapped reads = 2,563,024 (91.96%) number of supplementary alignments = 14,293 (0.51%) number of secondary alignments = 0 number of mapped bases = 149,927,096 bp number of sequenced bases = 149,882,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,246 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4806 >>>>>>> ACTG content number of A's = 36,371,976 bp (24.27%) number of C's = 29,085,023 bp (19.41%) number of T's = 46,982,468 bp (31.35%) number of G's = 37,441,255 bp (24.98%) number of N's = 1,892 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 764,044 number of insertions = 9,682 mapped reads with insertion percentage = 0.38% number of deletions = 28,067 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.4348X There is a 4.14% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11159540 0.04477236588309243 0.5887301694020506 chr2 243199373 15965881 0.06564935099565408 0.5204551908592148 chr3 198022430 11206154 0.056590326661479715 0.2949992131368065 chr4 191154276 8288176 0.04335856970314386 0.26727230966492077 chr5 180915260 7550564 0.04173536273280651 0.23227624060702873 chr6 171115067 8371889 0.048925492925763224 0.277440992757175 chr7 159138663 9380948 0.05894826450816669 1.0282776790559998 chr8 146364022 10640641 0.07269984012874421 0.4550800327293798 chr9 141213431 5912124 0.04186658420614396 0.2887524475667585 chr10 135534747 7243015 0.053440281258650225 0.6160942315523875 chr11 135006516 5139422 0.03806795517928927 0.29877656068309705 chr12 133851895 7108244 0.053105292233628816 0.31117620486379377 chr13 115169878 3908432 0.03393623461162301 0.20730177308192868 chr14 107349540 3765770 0.03507951687543328 0.22502014544337012 chr15 102531392 3640797 0.03550909559483987 0.2186388251957593 chr16 90354753 4661888 0.05159538203817568 0.2772490343489555 chr17 81195210 6484855 0.07986745769855143 0.3422100401264227 chr18 78077248 3494554 0.044757648220388094 0.4786186303720229 chr19 59128983 3046499 0.051522939266518415 0.5724730044626769 chr20 63025520 3409215 0.054092612008595886 0.2861471959913737 chr21 48129895 1554867 0.032305638730356676 0.22310609544257787 chr22 51304566 2286002 0.044557476619137566 0.24026507020284743 chrMT 16571 117191 7.072053587592783 4.875964293401833 chrX 155270560 5250256 0.03381359608672758 0.24984118825076912 chrY 59373566 340172 0.005729351004452049 0.1454419320688021