BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524722.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 = 799,302 number of mapped reads = 733,020 (91.71%) number of supplementary alignments = 3,490 (0.44%) number of secondary alignments = 0 number of mapped bases = 42,266,576 bp number of sequenced bases = 42,252,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,932 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9988 >>>>>>> ACTG content number of A's = 10,527,772 bp (24.92%) number of C's = 7,578,698 bp (17.94%) number of T's = 13,945,793 bp (33.01%) number of G's = 10,199,591 bp (24.14%) number of N's = 895 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 211,904 number of insertions = 2,591 mapped reads with insertion percentage = 0.35% number of deletions = 8,839 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.1582X There is a 1.29% 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 4045648 0.016231245417839903 0.23987204342226223 chr2 243199373 3387545 0.013929086075398722 0.1876213648442978 chr3 198022430 3586133 0.018109731306700964 0.14060288215730654 chr4 191154276 2362125 0.01235716537149292 0.11828439803450749 chr5 180915260 1851873 0.0102361348622554 0.1050495352494829 chr6 171115067 2590918 0.015141378520454893 0.13701972059038153 chr7 159138663 3044002 0.019127985258993913 0.25953017958201113 chr8 146364022 2410838 0.016471520576279326 0.16770838530623278 chr9 141213431 1367850 0.009686401571816494 0.12211406379477523 chr10 135534747 1964438 0.014493980646896401 0.15632461522985236 chr11 135006516 1878568 0.013914646904894575 0.14871137251896116 chr12 133851895 1806774 0.01349830721485116 0.12186926571532895 chr13 115169878 1270463 0.011031209045823597 0.11063033359235115 chr14 107349540 2200951 0.02050265888423928 0.15043777049522866 chr15 102531392 1115940 0.010883886176050355 0.11023028945061408 chr16 90354753 1055235 0.011678799011270608 0.1200507998701089 chr17 81195210 698373 0.008601160093064603 0.09776888575639416 chr18 78077248 886604 0.011355471955159076 0.2117643663355896 chr19 59128983 572398 0.009680497971696891 0.16387205335832689 chr20 63025520 734338 0.011651438972657425 0.11349082312412977 chr21 48129895 536494 0.011146793484589983 0.11352483587445324 chr22 51304566 308759 0.006018158305831882 0.0803071258950081 chrMT 16571 69243 4.178564962886972 2.898335705651807 chrX 155270560 2401074 0.01546380717632499 0.1346847267296663 chrY 59373566 119992 0.0020209667042737503 0.06884570617603077