BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716998.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 = 6,102,986 number of mapped reads = 5,564,563 (91.18%) number of supplementary alignments = 30,053 (0.49%) number of secondary alignments = 0 number of mapped bases = 321,725,300 bp number of sequenced bases = 321,636,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 484,576 duplication rate = 6.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6935 >>>>>>> ACTG content number of A's = 85,897,175 bp (26.71%) number of C's = 59,079,431 bp (18.37%) number of T's = 98,717,847 bp (30.69%) number of G's = 77,937,302 bp (24.23%) number of N's = 4,988 bp (0%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,713,359 number of insertions = 25,255 mapped reads with insertion percentage = 0.45% number of deletions = 53,345 mapped reads with deletion percentage = 0.95% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.1039X std coverageData = 0.8711X There is a 7.82% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 23530278 0.09440408976954966 1.8283391616929798 chr2 243199373 28432465 0.11691010815229363 0.9773964106024191 chr3 198022430 18849050 0.09518643923317172 0.38489423107006127 chr4 191154276 20534046 0.10742132705417481 0.5125042489492212 chr5 180915260 15658397 0.08655100183367616 0.3881911587969776 chr6 171115067 17288480 0.10103423563513551 0.5163272365608901 chr7 159138663 19417693 0.1220174446231209 1.081511501368142 chr8 146364022 14507380 0.09911848418595658 0.9240848661470612 chr9 141213431 12463429 0.08825951548475584 0.8645132766868744 chr10 135534747 11533460 0.08509596435812877 0.7992814570744752 chr11 135006516 12892932 0.0954985906013603 0.6694986114610554 chr12 133851895 22540409 0.16839813138245074 0.6746558089454032 chr13 115169878 12722434 0.11046667949062167 0.416559562484481 chr14 107349540 11378999 0.10599951336540427 0.48147806127358456 chr15 102531392 7930871 0.0773506615417842 0.34963507032168034 chr16 90354753 9556465 0.10576604641927359 0.4741187288527556 chr17 81195210 10089843 0.12426648074436904 0.49434602947201045 chr18 78077248 10644580 0.13633395480332502 1.6681866181882692 chr19 59128983 5799421 0.09808085148361169 1.2539657482684659 chr20 63025520 10612234 0.16837995148631857 0.5577948768968408 chr21 48129895 4089129 0.08496027261227143 0.4619216693523432 chr22 51304566 3113290 0.06068251313148229 0.2991687100446782 chrMT 16571 176113 10.627783477158893 6.365321689082174 chrX 155270560 17082616 0.11001838339476588 0.5921298822515669 chrY 59373566 881286 0.014843070062525806 0.30232087843521266