BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716152.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 = 934,905 number of mapped reads = 758,942 (81.18%) number of supplementary alignments = 2,894 (0.31%) number of secondary alignments = 0 number of mapped bases = 42,204,319 bp number of sequenced bases = 42,191,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,943 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4514 >>>>>>> ACTG content number of A's = 10,856,952 bp (25.73%) number of C's = 8,103,069 bp (19.21%) number of T's = 12,713,132 bp (30.13%) number of G's = 10,518,198 bp (24.93%) number of N's = 605 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 220,705 number of insertions = 3,438 mapped reads with insertion percentage = 0.45% number of deletions = 7,848 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.93% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1455X There is a 1.28% of reference with a coverageData >= 1X There is a 0.06% 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 3516116 0.014106749206454335 0.17221932252979652 chr2 243199373 4157529 0.017095146869478155 0.2056884812743932 chr3 198022430 2763306 0.013954510102719172 0.12468526601964042 chr4 191154276 2349771 0.012292536945393782 0.11866310808821068 chr5 180915260 2252694 0.012451652779317786 0.11658996505360465 chr6 171115067 2351989 0.013745072489729967 0.1301504015755084 chr7 159138663 2080039 0.013070607486503768 0.2111196409650533 chr8 146364022 3436564 0.0234795679501073 0.17117888054101627 chr9 141213431 1756389 0.012437832489177321 0.12497189628536018 chr10 135534747 1989974 0.014682389896666129 0.15712260099441763 chr11 135006516 1432531 0.010610828591414061 0.11739890639863484 chr12 133851895 1971201 0.014726732109395986 0.12745125757607031 chr13 115169878 1095226 0.009509656682973999 0.1027008756485709 chr14 107349540 1252134 0.011664083516333652 0.11438482787514684 chr15 102531392 1022972 0.009977158995364074 0.10881958209959051 chr16 90354753 1323468 0.01464746409079332 0.1297595706825385 chr17 81195210 1857361 0.022875253355462716 0.1630828912322188 chr18 78077248 959431 0.012288227679336239 0.15943076251970129 chr19 59128983 993041 0.01679448807702307 0.17586958280601822 chr20 63025520 912597 0.014479801197990909 0.12546369469820592 chr21 48129895 434936 0.00903671200612426 0.10154044069805096 chr22 51304566 660989 0.012883629110126377 0.119235328248152 chrMT 16571 26253 1.5842737312171866 1.5291388341653085 chrX 155270560 1506012 0.009699275896216256 0.11070663297939455 chrY 59373566 101796 0.0017145003552591063 0.05465835925171894