BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063522.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,702,773 number of mapped reads = 4,504,593 (95.79%) number of supplementary alignments = 33,868 (0.72%) number of secondary alignments = 0 number of mapped bases = 301,071,694 bp number of sequenced bases = 300,930,775 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 477,513 duplication rate = 8.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9579 >>>>>>> ACTG content number of A's = 82,779,942 bp (27.51%) number of C's = 54,875,299 bp (18.24%) number of T's = 97,106,827 bp (32.27%) number of G's = 66,132,505 bp (21.98%) number of N's = 36,202 bp (0.01%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,579,881 number of insertions = 19,761 mapped reads with insertion percentage = 0.43% number of deletions = 78,285 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.0973X std coverageData = 1.0146X There is a 7.11% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29735539 0.11929975893620742 2.3541844520362507 chr2 243199373 30406897 0.12502868171457004 0.922542359355172 chr3 198022430 16739038 0.08453102004656746 0.37520147900586903 chr4 191154276 18100204 0.09468898304948198 0.43097810393834296 chr5 180915260 14113339 0.07801077145178356 0.361117369676018 chr6 171115067 23975728 0.14011465162211578 0.5869000886489276 chr7 159138663 27258870 0.1712900528767167 1.4036476657022932 chr8 146364022 12651668 0.08643973995193983 1.7660801040117045 chr9 141213431 9811412 0.06947931178019462 0.7186976661032884 chr10 135534747 16920969 0.12484598506684046 0.7204437434030085 chr11 135006516 14660073 0.10858789215773852 0.5990760757882426 chr12 133851895 11226602 0.0838733138593219 0.42065912957743695 chr13 115169878 7144004 0.06203014298582482 0.3288228232438582 chr14 107349540 5900845 0.054968516865558995 0.40282259007274196 chr15 102531392 4900602 0.047796113018732836 0.3047417876824335 chr16 90354753 4431309 0.049043452091557374 0.362551495919115 chr17 81195210 8232223 0.10138803754556457 0.4500630642798043 chr18 78077248 5744747 0.07357773419472981 1.3446852262553781 chr19 59128983 6190787 0.10469970369691628 1.489956784547582 chr20 63025520 3549131 0.05631260162550027 0.3645608808841624 chr21 48129895 5456807 0.113376665376062 0.4680616800485077 chr22 51304566 3096013 0.06034575947879571 0.3058139557402074 chrMT 16571 626337 37.797175789029026 19.105191879607787 chrX 155270560 19304410 0.12432756087180982 0.5640694176354758 chrY 59373566 894140 0.01505956371224191 0.5881980965567075