BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524644.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 = 1,600,673 number of mapped reads = 1,487,644 (92.94%) number of supplementary alignments = 5,612 (0.35%) number of secondary alignments = 0 number of mapped bases = 87,189,143 bp number of sequenced bases = 87,166,245 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,890 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0614 >>>>>>> ACTG content number of A's = 22,002,063 bp (25.24%) number of C's = 17,837,751 bp (20.46%) number of T's = 26,257,693 bp (30.12%) number of G's = 21,066,062 bp (24.17%) number of N's = 2,676 bp (0%) GC percentage = 44.63% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 413,528 number of insertions = 5,800 mapped reads with insertion percentage = 0.39% number of deletions = 13,732 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2601X There is a 2.5% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6171680 0.024760941317775093 0.4396580971831394 chr2 243199373 7315956 0.030082133476553002 0.28161179285501164 chr3 198022430 5130296 0.025907650966610195 0.17482345364932783 chr4 191154276 5391536 0.028205155086355484 0.20804711106340476 chr5 180915260 4899571 0.027082132264575138 0.18028687905103202 chr6 171115067 4584359 0.026791089062893566 0.19059302446949838 chr7 159138663 5564872 0.03496869896412288 0.33105443797204004 chr8 146364022 3877503 0.026492186720586293 0.2823255637327586 chr9 141213431 3912151 0.02770381664333331 0.25617074575018156 chr10 135534747 3275971 0.024170709522924036 0.25186188803747056 chr11 135006516 3318301 0.024578821069643778 0.21633576353471526 chr12 133851895 6298407 0.047055045429128965 0.26373117188852846 chr13 115169878 3242151 0.028151032685820854 0.18226329160021604 chr14 107349540 3048362 0.02839660048846041 0.19698342496528662 chr15 102531392 2187005 0.02133010151661649 0.15844238194056623 chr16 90354753 2493708 0.02759907937549229 0.19098434364921313 chr17 81195210 2634917 0.032451631075281415 0.20644766312662305 chr18 78077248 2722035 0.034863357376530485 0.43753596224410757 chr19 59128983 1491748 0.02522871059696731 0.33431886960208956 chr20 63025520 2787946 0.04423519234748083 0.23462595739456 chr21 48129895 1064867 0.02212485607957383 0.18376778122789436 chr22 51304566 887077 0.01729041037010234 0.14246468942390625 chrMT 16571 5872 0.35435399191358397 0.6370309150006233 chrX 155270560 4631643 0.029829498908228322 0.21249524445402862 chrY 59373566 251209 0.004230990606156282 0.11406877230410892