BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524996.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 = 4,150,052 number of mapped reads = 3,720,791 (89.66%) number of supplementary alignments = 11,418 (0.28%) number of secondary alignments = 0 number of mapped bases = 211,664,300 bp number of sequenced bases = 211,598,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,684 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2487 >>>>>>> ACTG content number of A's = 54,483,618 bp (25.75%) number of C's = 36,799,752 bp (17.39%) number of T's = 66,992,760 bp (31.66%) number of G's = 53,319,873 bp (25.2%) number of N's = 2,046 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,046,998 number of insertions = 14,814 mapped reads with insertion percentage = 0.4% number of deletions = 40,206 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0684X std coverageData = 0.5417X There is a 5.66% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.16% 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 0.01% 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 22584269 0.0906086769589232 1.0837512359039483 chr2 243199373 19985952 0.08217929081585255 0.6614241118306383 chr3 198022430 11741210 0.059292323601927314 0.29545641326318234 chr4 191154276 13430591 0.07026047902794495 0.3695614197171438 chr5 180915260 9157030 0.05061502274600827 0.2762415498118806 chr6 171115067 17239752 0.1007494681926519 0.6112628025246788 chr7 159138663 13347458 0.08387313144637894 0.759915490760887 chr8 146364022 13105926 0.08954335786153786 0.5083392344656356 chr9 141213431 5796968 0.041051109366502116 0.4076396784642514 chr10 135534747 10840577 0.07998374763631647 0.5179620511770647 chr11 135006516 9016546 0.0667860060917356 0.46305269442501357 chr12 133851895 9086739 0.06788651740791567 0.31577310156001387 chr13 115169878 4071386 0.035351135823900065 0.22886244670314068 chr14 107349540 4734562 0.044104166631734054 0.26335733266091405 chr15 102531392 5972255 0.05824806318829652 0.3323990466362171 chr16 90354753 6843732 0.07574291083502824 0.3563739927437895 chr17 81195210 5348981 0.06587803640140841 0.4677237684896944 chr18 78077248 4234931 0.05424026984147802 0.6857385504886907 chr19 59128983 5273826 0.08919189426951585 0.6398666585624335 chr20 63025520 5097337 0.08087734936578071 0.34201988695701774 chr21 48129895 2495928 0.05185816424490434 0.3011411122260901 chr22 51304566 2779355 0.05417363826837557 0.2710938508259806 chrMT 16571 51543 3.1104338905316515 2.5549684556736243 chrX 155270560 8876323 0.057166812562536 0.3728318310609232 chrY 59373566 551123 0.009282295761046255 0.2222046248160215