BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524406.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 = 4,178,948 number of mapped reads = 3,777,339 (90.39%) number of supplementary alignments = 14,587 (0.35%) number of secondary alignments = 0 number of mapped bases = 222,654,521 bp number of sequenced bases = 222,589,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 257,739 duplication rate = 5.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0401 >>>>>>> ACTG content number of A's = 57,824,978 bp (25.98%) number of C's = 43,544,815 bp (19.56%) number of T's = 69,162,676 bp (31.07%) number of G's = 52,027,374 bp (23.37%) number of N's = 29,623 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,074,556 number of insertions = 16,537 mapped reads with insertion percentage = 0.44% number of deletions = 41,018 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.48% >>>>>>> Coverage mean coverageData = 0.0719X std coverageData = 0.6627X There is a 5.83% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 18701255 0.07502992339585786 1.5437543341098174 chr2 243199373 18066786 0.07428796290523332 0.6991289951021664 chr3 198022430 15435391 0.07794769006723128 0.32906238650763164 chr4 191154276 14878777 0.07783648533187926 0.40452144167478266 chr5 180915260 13432482 0.07424736862993205 0.32502029893317813 chr6 171115067 8588276 0.050190063041029576 0.3081974385855475 chr7 159138663 12754168 0.08014499908171278 0.9738280471589696 chr8 146364022 11735954 0.08018332538033152 0.5869701574939838 chr9 141213431 8226426 0.05825526610142345 0.45740195991059984 chr10 135534747 11056202 0.08157466808124118 0.542886121970117 chr11 135006516 9192614 0.06809015055243704 0.4890472059303221 chr12 133851895 10460289 0.07814823241762846 0.3504367097357118 chr13 115169878 7187907 0.06241134509146567 0.2961284750613389 chr14 107349540 6202212 0.05777586005491966 0.304162393870555 chr15 102531392 6823849 0.06655375360552991 0.3074992302790583 chr16 90354753 6696575 0.0741142527388681 0.3532687866680831 chr17 81195210 5972758 0.07356047234806093 0.38778364767191326 chr18 78077248 6091763 0.07802225559999246 0.9051339801687224 chr19 59128983 6006524 0.10158341468514688 0.9802295177896531 chr20 63025520 6223109 0.09873951059824655 0.39666025699930246 chr21 48129895 3091411 0.06423057852089642 0.3639713195052285 chr22 51304566 1527176 0.029766863245661215 0.20200171580409026 chrMT 16571 412609 24.899462917144408 13.363615084199761 chrX 155270560 13204635 0.08504274731797193 0.4203605825372638 chrY 59373566 685373 0.011543403001935239 0.29811367234231295