BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173956.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,024,502 number of mapped reads = 3,919,200 (97.38%) number of supplementary alignments = 510,589 (12.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,963,271 number of mapped paired reads (second in pair) = 1,955,929 number of mapped paired reads (both in pair) = 3,851,442 number of mapped paired reads (singletons) = 67,758 number of mapped bases = 445,697,053 bp number of sequenced bases = 445,395,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,110,487 duplication rate = 64.28% >>>>>>> Insert size mean insert size = 1,099,087.9211 std insert size = 9,754,363.7501 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 52.4843 >>>>>>> ACTG content number of A's = 132,258,755 bp (29.69%) number of C's = 89,119,942 bp (20.01%) number of T's = 131,132,527 bp (29.44%) number of G's = 92,880,589 bp (20.85%) number of N's = 3,546 bp (0%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 3,979,127 number of insertions = 50,338 mapped reads with insertion percentage = 1.23% number of deletions = 125,156 mapped reads with deletion percentage = 3.11% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.144X std coverageData = 2.791X There is a 3.14% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 1.77% of reference with a coverageData >= 3X There is a 1.42% of reference with a coverageData >= 4X There is a 1.05% of reference with a coverageData >= 5X There is a 0.86% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 37158145 0.14907944803074333 1.7379609269001468 chr2 243199373 37629228 0.15472584298151132 8.735737013735074 chr3 198022430 32003076 0.16161338894790858 1.1888807349308383 chr4 191154276 30660340 0.16039578418847403 1.5726942905273738 chr5 180915260 28087283 0.155251044052337 1.1728053457067293 chr6 171115067 24271069 0.14184063055066917 1.2173388483718863 chr7 159138663 26527618 0.1666949910217607 1.6069923712433698 chr8 146364022 24244770 0.16564706045041588 1.8567106618663376 chr9 141213431 18566634 0.13147923585257268 1.3753592314835743 chr10 135534747 18560554 0.1369431412300493 1.8467509893266978 chr11 135006516 20519583 0.15198957508095387 1.170222113752968 chr12 133851895 18971778 0.14173708934042362 1.1458236622340088 chr13 115169878 15298430 0.1328336042867042 1.0874389168306584 chr14 107349540 13360723 0.12445999302838186 1.0490941764373445 chr15 102531392 12991690 0.12670938867191037 1.0603174962619797 chr16 90354753 14147913 0.1565818347154355 1.378343805355884 chr17 81195210 13638836 0.16797586951249957 1.2758214553058411 chr18 78077248 11705290 0.14991934654254208 1.7354247042352466 chr19 59128983 9218095 0.15589808131825977 1.3766523673179347 chr20 63025520 9468959 0.15024007735279296 1.1646270559015477 chr21 48129895 6524543 0.13556113097691155 1.2806767909029138 chr22 51304566 5582460 0.10881019829697029 1.0480703381956815 chrMT 16571 1137968 68.67225876531289 58.476371934749864 chrX 155270560 12026634 0.07745598392895602 0.8142869650666295 chrY 59373566 3395434 0.057187638013859565 1.0222204237415182