BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716161.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 = 3,507,559 number of mapped reads = 3,166,109 (90.27%) number of supplementary alignments = 12,800 (0.36%) number of secondary alignments = 0 number of mapped bases = 181,314,231 bp number of sequenced bases = 181,266,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,110 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.172 >>>>>>> ACTG content number of A's = 48,122,065 bp (26.55%) number of C's = 33,774,136 bp (18.63%) number of T's = 55,052,911 bp (30.37%) number of G's = 44,314,579 bp (24.45%) number of N's = 2,801 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 974,412 number of insertions = 13,450 mapped reads with insertion percentage = 0.42% number of deletions = 28,586 mapped reads with deletion percentage = 0.9% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.5031X There is a 4.87% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 12885836 0.05169831051293549 0.8183013695071132 chr2 243199373 15401901 0.06333034830644896 0.6170237792267029 chr3 198022430 10611798 0.05358886869532911 0.2668358105798913 chr4 191154276 11215052 0.05867016022178861 0.3258517719677222 chr5 180915260 9851874 0.05445573800684365 0.2756146272445251 chr6 171115067 9084314 0.05308891939948222 0.31586342845409227 chr7 159138663 12021556 0.0755413912205609 0.7446728273912544 chr8 146364022 7636293 0.05217329296949765 0.4349340659245347 chr9 141213431 8291371 0.05871517277984698 0.5845897819648437 chr10 135534747 7033676 0.05189574006435412 0.453000147659258 chr11 135006516 6929918 0.051330248385937166 0.435306267063651 chr12 133851895 13135123 0.09813176720434179 0.4422405450834217 chr13 115169878 6712150 0.058280429888099734 0.2788334014903359 chr14 107349540 6682232 0.06224742090185016 0.35063974836215167 chr15 102531392 4648245 0.04533484730218039 0.24806692485115153 chr16 90354753 5404775 0.05981727380738897 0.33707880496459985 chr17 81195210 5612165 0.06911940987651857 0.3258873490322232 chr18 78077248 5711627 0.07315353891571588 1.1322560437207285 chr19 59128983 3083826 0.05215422020703451 0.6674977864863352 chr20 63025520 5093144 0.08081082075959072 0.3546169576676227 chr21 48129895 2082421 0.0432666848743385 0.3076043705456193 chr22 51304566 1759003 0.034285505894348665 0.21057372456651374 chrMT 16571 27445 1.6562066260334318 1.724496195938565 chrX 155270560 9883622 0.0636541917540582 0.3922375638008565 chrY 59373566 514864 0.00867160311711781 0.18754027538400775