BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716712.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 = 4,370,063 number of mapped reads = 4,129,429 (94.49%) number of supplementary alignments = 90,647 (2.07%) number of secondary alignments = 0 number of mapped bases = 317,860,685 bp number of sequenced bases = 317,741,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 330,824 duplication rate = 6.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8445 >>>>>>> ACTG content number of A's = 79,654,097 bp (25.07%) number of C's = 64,699,477 bp (20.36%) number of T's = 92,213,092 bp (29.02%) number of G's = 81,162,999 bp (25.54%) number of N's = 12,271 bp (0%) GC percentage = 45.91% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,003,697 number of insertions = 26,581 mapped reads with insertion percentage = 0.63% number of deletions = 56,848 mapped reads with deletion percentage = 1.35% homopolymer indels = 38.49% >>>>>>> Coverage mean coverageData = 0.1027X std coverageData = 0.6621X There is a 7.34% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 25820098 0.1035909074023932 0.9934773535157085 chr2 243199373 26856206 0.11042876331757648 0.7787242072542812 chr3 198022430 20422287 0.10313118064453608 0.42660939086599403 chr4 191154276 20057138 0.10492644171872985 0.6793911280734708 chr5 180915260 18742967 0.10360080736141329 0.43214368873956616 chr6 171115067 17813049 0.10409982774924198 0.45887640846909067 chr7 159138663 17188212 0.10800776929990923 0.7885046636023727 chr8 146364022 16152444 0.11035802227408044 0.7099766856182851 chr9 141213431 12982120 0.09193261510656164 0.6143585952608129 chr10 135534747 15465513 0.11410736613541618 0.9187470651260821 chr11 135006516 14555042 0.10780992230034289 0.7340396900434525 chr12 133851895 14242954 0.10640831046882078 0.44589763023273005 chr13 115169878 9646264 0.08375683093108773 0.38786826697146254 chr14 107349540 9654057 0.08993105140459848 0.4767502520956603 chr15 102531392 9464631 0.09230959236367337 0.40913718307432795 chr16 90354753 9945946 0.11007662208981966 0.5116099363670225 chr17 81195210 9110928 0.11221016609231013 0.5419115316147769 chr18 78077248 8307934 0.10640659363403793 1.0093950151225999 chr19 59128983 6974476 0.11795359307972539 0.7643324781161512 chr20 63025520 7292766 0.11571131820887792 0.5107153071798232 chr21 48129895 4296161 0.08926179872197934 0.5865675372470259 chr22 51304566 4290437 0.08362680623786975 0.4142466908075812 chrMT 16571 33619 2.028785227204152 2.2002045825584213 chrX 155270560 17511594 0.11278116083306455 0.5222379649511188 chrY 59373566 1033842 0.017412496328753437 0.6412018996172283