BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716863.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 = 1,529,179 number of mapped reads = 1,419,781 (92.85%) number of supplementary alignments = 30,832 (2.02%) number of secondary alignments = 0 number of mapped bases = 109,427,777 bp number of sequenced bases = 109,383,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,300 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4062 >>>>>>> ACTG content number of A's = 27,889,811 bp (25.5%) number of C's = 22,106,956 bp (20.21%) number of T's = 32,976,303 bp (30.15%) number of G's = 26,406,015 bp (24.14%) number of N's = 4,367 bp (0%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 731,179 number of insertions = 9,591 mapped reads with insertion percentage = 0.66% number of deletions = 21,309 mapped reads with deletion percentage = 1.47% homopolymer indels = 38.42% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.3019X There is a 3.02% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11787307 0.047290983479635944 0.5559332646064895 chr2 243199373 11013428 0.04528559372560553 0.3282872896303977 chr3 198022430 6910574 0.03489793555204832 0.21453667684059358 chr4 191154276 5183525 0.02711697121543857 0.2596915061370695 chr5 180915260 6389280 0.03531642383290387 0.21727861565570697 chr6 171115067 6434393 0.03760272612346872 0.2308642207704903 chr7 159138663 6644563 0.04175329159325663 0.38631737708003006 chr8 146364022 6782694 0.0463412654784794 0.328216935192184 chr9 141213431 3192577 0.022608168198958355 0.21040643860976313 chr10 135534747 5772184 0.0425882227824574 0.4139112282954752 chr11 135006516 4492319 0.03327483097186213 0.25287956643087434 chr12 133851895 3810138 0.028465327293274407 0.19184195029994114 chr13 115169878 2063915 0.017920614624598284 0.1479689991738002 chr14 107349540 2071006 0.019292173958081235 0.16318704501368472 chr15 102531392 2255505 0.021998189588609118 0.16733273417913505 chr16 90354753 3187975 0.03528286995593912 0.22657705144419604 chr17 81195210 2024289 0.024931138179210326 0.20195604139727139 chr18 78077248 3179194 0.040718571433255434 0.3219242417793814 chr19 59128983 2632120 0.0445148870563189 0.40715678887635337 chr20 63025520 2805069 0.044506875944855355 0.25204897164052087 chr21 48129895 1817173 0.03775559867728778 0.26052565708376674 chr22 51304566 1689453 0.03292987606600161 0.2124811135873425 chrMT 16571 34043 2.0543720958300646 2.1326353310361528 chrX 155270560 6886166 0.044349463285248664 0.25003538868189235 chrY 59373566 368887 0.006212983737577763 0.22274197820581781