BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,278,529 number of mapped reads = 4,037,342 (94.36%) number of supplementary alignments = 24,663 (0.58%) number of secondary alignments = 0 number of mapped bases = 260,268,134 bp number of sequenced bases = 260,170,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 679,788 duplication rate = 13.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7105 >>>>>>> ACTG content number of A's = 67,660,496 bp (26.01%) number of C's = 46,308,434 bp (17.8%) number of T's = 85,683,477 bp (32.93%) number of G's = 60,490,144 bp (23.25%) number of N's = 28,238 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,398,250 number of insertions = 17,117 mapped reads with insertion percentage = 0.42% number of deletions = 55,971 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 0.0841X std coverageData = 0.8587X There is a 5.55% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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% 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 26089535 0.1046718956820573 1.6046725937994677 chr2 243199373 27032911 0.11115534825001379 1.529702233052099 chr3 198022430 13808091 0.0697299341291792 0.37709607180914584 chr4 191154276 15576123 0.08148456485482962 0.46064635872942705 chr5 180915260 12503472 0.06911231258214481 0.37871996105118616 chr6 171115067 15829112 0.09250565877988991 0.6010553485361521 chr7 159138663 24388763 0.15325479390259802 0.8452073845126152 chr8 146364022 9281705 0.06341520869110853 0.9800980025119619 chr9 141213431 9608438 0.068041955584239 0.8577212493119765 chr10 135534747 14504501 0.10701684491283996 0.6440332361436301 chr11 135006516 11462142 0.08490065768381135 0.5542784603987068 chr12 133851895 9126370 0.0681825983860744 0.4676607224173802 chr13 115169878 3748174 0.032544742297981766 0.3297439577680746 chr14 107349540 5928594 0.05522700889076935 0.4182260181172891 chr15 102531392 4044182 0.039443354090033224 0.31551263950483915 chr16 90354753 4060195 0.04493615294371952 0.39205168590913836 chr17 81195210 8577940 0.10564588723891472 0.5204992981430518 chr18 78077248 7337899 0.09398255174157778 1.4422682651510095 chr19 59128983 5127634 0.08671946886013582 1.0556628820619371 chr20 63025520 4024958 0.06386235290085666 0.38556193665016947 chr21 48129895 2962581 0.06155386376803856 0.39950168206762465 chr22 51304566 2686200 0.052357912938977014 0.31514497774953515 chrMT 16571 549797 33.178263230945625 20.416211224147087 chrX 155270560 21288183 0.1371037948211174 0.6694063019801227 chrY 59373566 720634 0.012137286818851338 0.28253875097164993