BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716514.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 = 2,962,696 number of mapped reads = 2,711,711 (91.53%) number of supplementary alignments = 16,681 (0.56%) number of secondary alignments = 0 number of mapped bases = 158,183,619 bp number of sequenced bases = 158,139,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,595 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1341 >>>>>>> ACTG content number of A's = 39,793,157 bp (25.16%) number of C's = 31,936,846 bp (20.2%) number of T's = 48,242,304 bp (30.51%) number of G's = 38,164,830 bp (24.13%) number of N's = 2,098 bp (0%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 788,616 number of insertions = 8,307 mapped reads with insertion percentage = 0.3% number of deletions = 28,294 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.4677X There is a 4.34% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 12928964 0.05187134117511386 0.6332205902454264 chr2 243199373 15493879 0.06370854829465371 0.527731532619655 chr3 198022430 12095995 0.06108396407417079 0.31307886679379293 chr4 191154276 8826931 0.04617699998508011 0.26746052615901084 chr5 180915260 7907017 0.04370563876148424 0.2402134257456434 chr6 171115067 8751838 0.05114592276085191 0.2886045590459899 chr7 159138663 9809191 0.06163926989885544 1.1918620886077456 chr8 146364022 11706329 0.07998091908132997 0.4816111643982422 chr9 141213431 6609030 0.04680170967590186 0.3137237589808841 chr10 135534747 7761288 0.05726419366098053 0.619436646980992 chr11 135006516 4622467 0.03423884370144031 0.2986430806656987 chr12 133851895 7327001 0.05473961351088828 0.30924088545233674 chr13 115169878 4102491 0.03562121512362807 0.21391797679875063 chr14 107349540 5055231 0.04709131496977071 0.25705519216315253 chr15 102531392 3572475 0.03484274357652337 0.2286661018632313 chr16 90354753 4751602 0.05258829051306244 0.27971652335316505 chr17 81195210 6593638 0.08120722885007625 0.34673492727823485 chr18 78077248 3687832 0.04723311969192357 0.5254595660443472 chr19 59128983 3092451 0.05230008775899291 0.5669980009111197 chr20 63025520 3487802 0.0553395196104689 0.29403249341847576 chr21 48129895 1618523 0.03362822628223062 0.2206455944308706 chr22 51304566 2301155 0.044852830447878654 0.2421668394742227 chrMT 16571 163261 9.852211695130046 6.049525693052872 chrX 155270560 5585008 0.03596952313432759 0.2699508701085446 chrY 59373566 332220 0.005595419348738461 0.12941147104702852