BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173897.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 = 1,841,664 number of mapped reads = 1,790,072 (97.2%) number of supplementary alignments = 170,563 (9.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 895,985 number of mapped paired reads (second in pair) = 894,087 number of mapped paired reads (both in pair) = 1,758,274 number of mapped paired reads (singletons) = 31,798 number of mapped bases = 212,440,485 bp number of sequenced bases = 212,321,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,414,577 duplication rate = 64.96% >>>>>>> Insert size mean insert size = 1,004,055.4454 std insert size = 9,285,821.0558 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 52.9757 >>>>>>> ACTG content number of A's = 63,998,160 bp (30.14%) number of C's = 41,566,711 bp (19.58%) number of T's = 63,732,119 bp (30.02%) number of G's = 43,022,473 bp (20.26%) number of N's = 2,118 bp (0%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 2,265,315 number of insertions = 24,500 mapped reads with insertion percentage = 1.31% number of deletions = 46,952 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0686X std coverageData = 1.1833X There is a 1.37% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% 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 0.05% 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% 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 18259132 0.0732561143749367 0.9936496947680565 chr2 243199373 18836917 0.07745462814166054 3.0012897888919086 chr3 198022430 13444208 0.06789234936668538 0.7745492015804635 chr4 191154276 14182893 0.07419605408146873 0.938403407853916 chr5 180915260 12987606 0.07178833891624178 0.7931994677722105 chr6 171115067 12213347 0.07137505313895007 0.8403185483925193 chr7 159138663 12217344 0.07677168935370533 0.9353526302300005 chr8 146364022 11126924 0.07602226180966795 1.0385304306237513 chr9 141213431 8769942 0.062104163448871944 0.8621817391642993 chr10 135534747 10831363 0.07991576506945484 1.0983012458770642 chr11 135006516 9464270 0.07010232009838696 0.7839585263031865 chr12 133851895 9330836 0.06971015240389387 0.7792400341373431 chr13 115169878 7964675 0.06915588640286656 0.7961172749762383 chr14 107349540 6569208 0.061194561243578686 0.7349114870110358 chr15 102531392 6023375 0.05874664219910328 0.7075810766212554 chr16 90354753 6121449 0.06774905355559989 0.8310144307005973 chr17 81195210 5574981 0.0686614518270228 0.7807362106693951 chr18 78077248 6080896 0.07788307292798025 1.0921383900063444 chr19 59128983 3930784 0.0664781263022907 0.8172959714600742 chr20 63025520 4575100 0.0725912297113931 0.8019909796519105 chr21 48129895 2978715 0.061889081619646166 0.8608142675892707 chr22 51304566 2469184 0.0481279580456835 0.6829324226356627 chrMT 16571 624869 37.708587291050634 31.927449020811974 chrX 155270560 6079168 0.039152096830204 0.5844218712205146 chrY 59373566 1783299 0.030035234872030424 0.6578272579616619