BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524284.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 = 3,602,914 number of mapped reads = 3,345,824 (92.86%) number of supplementary alignments = 12,435 (0.35%) number of secondary alignments = 0 number of mapped bases = 196,238,666 bp number of sequenced bases = 196,180,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 226,310 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2159 >>>>>>> ACTG content number of A's = 49,214,606 bp (25.09%) number of C's = 38,079,763 bp (19.41%) number of T's = 61,444,537 bp (31.32%) number of G's = 47,417,228 bp (24.17%) number of N's = 24,559 bp (0.01%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 946,830 number of insertions = 11,985 mapped reads with insertion percentage = 0.36% number of deletions = 36,569 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 0.0634X std coverageData = 0.5902X There is a 5.25% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 15834569 0.06352870430762136 1.2620966162793126 chr2 243199373 16381049 0.06735646065995408 0.6053788948128257 chr3 198022430 13066701 0.06598596431727456 0.3011002561811354 chr4 191154276 12652780 0.06619145678959334 0.35797748370377447 chr5 180915260 11957022 0.06609183769240914 0.30679702815805493 chr6 171115067 11276993 0.06590298094556454 0.3480608130357593 chr7 159138663 10815633 0.06796357840457665 0.8816253791746295 chr8 146364022 9977321 0.06816785206954754 0.5467760754539079 chr9 141213431 8216090 0.058182071930537545 0.5136288813570081 chr10 135534747 9429441 0.06957212972109654 0.5167718646735244 chr11 135006516 9047936 0.06701851338790196 0.5271572752209417 chr12 133851895 8774514 0.06555390194513122 0.31550610265744466 chr13 115169878 6169954 0.05357263641453193 0.2722918948014029 chr14 107349540 5996751 0.055861916129309915 0.3100522401356572 chr15 102531392 5587981 0.054500196388633834 0.2738543836900921 chr16 90354753 5624245 0.06224625504759002 0.3405873678982949 chr17 81195210 5279367 0.06502067055433443 0.34203284404156403 chr18 78077248 5376294 0.06885865137049912 1.1005030999893257 chr19 59128983 3896995 0.06590668065439245 0.781816840718911 chr20 63025520 4171360 0.06618525321171487 0.31451625100328773 chr21 48129895 2592109 0.05385652721660831 0.32574295087899496 chr22 51304566 2329589 0.045407050124934296 0.24762803496157532 chrMT 16571 65598 3.958602377647698 2.866019004775854 chrX 155270560 11121404 0.07162596695729055 0.3961791999589061 chrY 59373566 596970 0.010054474410379865 0.2443809617118174