BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926890.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,725,404 number of mapped reads = 20,230,127 (93.12%) number of supplementary alignments = 693,302 (3.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,162,121 number of mapped paired reads (second in pair) = 10,068,006 number of mapped paired reads (both in pair) = 19,841,206 number of mapped paired reads (singletons) = 388,921 number of mapped bases = 1,829,756,632 bp number of sequenced bases = 1,828,321,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,596,306 duplication rate = 6.48% >>>>>>> Insert size mean insert size = 385,969.0728 std insert size = 6,116,235.3357 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.299 >>>>>>> ACTG content number of A's = 518,700,930 bp (28.37%) number of C's = 357,280,088 bp (19.54%) number of T's = 526,226,983 bp (28.78%) number of G's = 425,964,024 bp (23.3%) number of N's = 149,030 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 19,086,686 number of insertions = 316,980 mapped reads with insertion percentage = 1.54% number of deletions = 975,531 mapped reads with deletion percentage = 4.7% homopolymer indels = 51.71% >>>>>>> Coverage mean coverageData = 0.5911X std coverageData = 1.9437X There is a 27.79% of reference with a coverageData >= 1X There is a 13.46% of reference with a coverageData >= 2X There is a 6.9% of reference with a coverageData >= 3X There is a 3.88% of reference with a coverageData >= 4X There is a 2.29% of reference with a coverageData >= 5X There is a 1.4% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.58% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 153448788 0.6156405443820339 1.817108674425798 chr2 243199373 158583032 0.652070069276042 2.7547114134276316 chr3 198022430 124743089 0.6299442391450302 1.3949415068906934 chr4 191154276 107917953 0.5645594503991112 1.4899435421795464 chr5 180915260 109455010 0.6050070624224845 1.3461365705764001 chr6 171115067 103149760 0.6028093364799957 1.5030647128131036 chr7 159138663 96567683 0.6068147185577398 1.4428240771039154 chr8 146364022 93830576 0.6410767804672654 1.465314726732616 chr9 141213431 80295747 0.5686126767927621 2.181080110647071 chr10 135534747 91360955 0.6740777329963954 4.6544959000159105 chr11 135006516 86071548 0.6375362504725327 1.5492267305714775 chr12 133851895 78916659 0.5895819330761063 1.44850190943896 chr13 115169878 54770794 0.47556526889782763 1.195985837378069 chr14 107349540 55758596 0.5194115969197446 1.282626255936902 chr15 102531392 56342735 0.5495169225830856 1.389924111079254 chr16 90354753 55402101 0.6131619993471732 2.6347788476266016 chr17 81195210 46737529 0.5756192883792036 1.4281392401363344 chr18 78077248 48723808 0.6240461753979853 2.073629813005724 chr19 59128983 31702679 0.5361614117394848 1.4543290255719956 chr20 63025520 43978122 0.6977827711695199 1.5719812578210965 chr21 48129895 23430279 0.4868134243800033 1.763629653169393 chr22 51304566 24333937 0.47430353469903636 1.318891641012008 chrMT 16571 77002 4.64679258946352 4.028434668956921 chrX 155270560 101059115 0.6508581858660135 1.4539346232810801 chrY 59373566 3099135 0.052197218539981244 1.3090246972901887