BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354852.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 22,661,322 number of mapped reads = 22,431,572 (98.99%) number of supplementary alignments = 390,945 (1.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,238,188 number of mapped paired reads (second in pair) = 11,193,384 number of mapped paired reads (both in pair) = 22,338,382 number of mapped paired reads (singletons) = 93,190 number of mapped bases = 3,130,708,073 bp number of sequenced bases = 3,128,843,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,159,774 duplication rate = 26.77% >>>>>>> Insert size mean insert size = 133,878.295 std insert size = 4,051,200.6975 median insert size = 291 >>>>>>> Mapping quality mean mapping quality = 53.9606 >>>>>>> ACTG content number of A's = 901,278,818 bp (28.81%) number of C's = 655,788,131 bp (20.96%) number of T's = 907,287,998 bp (29%) number of G's = 664,436,146 bp (21.24%) number of N's = 52,128 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 27,266,397 number of insertions = 610,629 mapped reads with insertion percentage = 2.48% number of deletions = 579,964 mapped reads with deletion percentage = 2.41% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 1.0113X std coverageData = 19.8069X There is a 43.99% of reference with a coverageData >= 1X There is a 24.53% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 6.31% of reference with a coverageData >= 4X There is a 3.02% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% 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 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 253072320 1.0153327561819796 28.47422099805093 chr2 243199373 272806848 1.1217415762005274 38.15046633314758 chr3 198022430 200693822 1.0134903505628126 1.9092566668543485 chr4 191154276 221769588 1.16016022576445 29.111127281515508 chr5 180915260 182764360 1.0102208072442314 1.6521879421353216 chr6 171115067 173159351 1.0119468380887815 3.650649918155093 chr7 159138663 165175892 1.037936909146962 12.939417882496787 chr8 146364022 155903032 1.0651731885312634 23.2526814256513 chr9 141213431 132056585 0.9351559838525558 14.279518917395903 chr10 135534747 178725198 1.3186669983602064 36.61513941449338 chr11 135006516 142077452 1.052374775747861 4.226909270527381 chr12 133851895 134943357 1.0081542513835908 1.6813115067602789 chr13 115169878 94904249 0.8240370715683141 1.3986121084453802 chr14 107349540 92392356 0.8606683922446244 2.3866335373274046 chr15 102531392 87062534 0.849130517997844 1.4176576499840718 chr16 90354753 96668492 1.0698772205154499 7.419586891081972 chr17 81195210 84688377 1.043021835894014 5.616089167220177 chr18 78077248 86690172 1.1103128532399094 16.695671241668904 chr19 59128983 60643048 1.0256061397166258 15.673937149561153 chr20 63025520 65989343 1.047025760358661 9.285359776200217 chr21 48129895 44969409 0.934334242781955 14.690329264946428 chr22 51304566 38784810 0.7559718953669737 2.7976844698925802 chrMT 16571 29127831 1757.7593989499728 524.104249469965 chrX 155270560 83175734 0.5356825788481732 1.642401705997203 chrY 59373566 52463913 0.8836240861800351 30.875255118455065