BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716513.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 = 1,573,791 number of mapped reads = 1,435,587 (91.22%) number of supplementary alignments = 8,292 (0.53%) number of secondary alignments = 0 number of mapped bases = 82,926,725 bp number of sequenced bases = 82,905,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,609 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0134 >>>>>>> ACTG content number of A's = 21,232,952 bp (25.61%) number of C's = 16,631,700 bp (20.06%) number of T's = 25,421,612 bp (30.66%) number of G's = 19,617,822 bp (23.66%) number of N's = 975 bp (0%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 404,757 number of insertions = 6,623 mapped reads with insertion percentage = 0.46% number of deletions = 13,874 mapped reads with deletion percentage = 0.96% homopolymer indels = 40.03% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2558X There is a 2.41% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7117283 0.02855472524579989 0.36383014300997063 chr2 243199373 8475975 0.03485196074086918 0.32157463869683744 chr3 198022430 6120875 0.030910008527821824 0.19853346102887617 chr4 191154276 4767479 0.024940477920567156 0.18024009678746122 chr5 180915260 4664813 0.025784519227399612 0.17418947078523012 chr6 171115067 4800996 0.02805712018334423 0.19631300166378465 chr7 159138663 4202551 0.026408108003270078 0.5008247234025794 chr8 146364022 6123637 0.041838403429498544 0.2847843664969511 chr9 141213431 2883887 0.020422186328721097 0.17965340134995098 chr10 135534747 3990087 0.029439587178334423 0.3134096444350324 chr11 135006516 2985343 0.022112584551104184 0.19168959173836736 chr12 133851895 3794223 0.02834642722092205 0.19376262965019034 chr13 115169878 2238789 0.019439015121644913 0.15225942894809083 chr14 107349540 2179446 0.020302331989498976 0.1600428500580509 chr15 102531392 2059523 0.020086755478751328 0.1581375396928154 chr16 90354753 2644461 0.02926753615274672 0.19372716376056234 chr17 81195210 2759908 0.033991019913613134 0.20373940668746482 chr18 78077248 2013567 0.025789420754174123 0.28759588797876373 chr19 59128983 1772267 0.029972898400772427 0.3257414750553921 chr20 63025520 1943908 0.030843188600427257 0.19688925091137907 chr21 48129895 881421 0.018313378826195235 0.1507724283213992 chr22 51304566 1200472 0.023398931003529005 0.1667945960482417 chrMT 16571 116178 7.010922696276628 4.560889862574756 chrX 155270560 3010073 0.019385986628759504 0.17054732987568605 chrY 59373566 179563 0.0030242919887951483 0.07785720620628163