BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716995.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 = 1,384,206 number of mapped reads = 1,218,409 (88.02%) number of supplementary alignments = 4,836 (0.35%) number of secondary alignments = 0 number of mapped bases = 69,805,648 bp number of sequenced bases = 69,783,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,475 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8673 >>>>>>> ACTG content number of A's = 16,581,156 bp (23.76%) number of C's = 13,954,620 bp (20%) number of T's = 22,660,576 bp (32.47%) number of G's = 16,586,800 bp (23.77%) number of N's = 477 bp (0%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 370,103 number of insertions = 5,529 mapped reads with insertion percentage = 0.45% number of deletions = 13,742 mapped reads with deletion percentage = 1.12% homopolymer indels = 38.69% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2033X There is a 2.05% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 5598531 0.022461452563442157 0.24774448299260177 chr2 243199373 5804234 0.02386615527993158 0.2913352947386997 chr3 198022430 4667067 0.023568375562303723 0.16620310352381376 chr4 191154276 4455423 0.02330799547481742 0.18239861482890662 chr5 180915260 4132607 0.022842777331221257 0.16295011152325167 chr6 171115067 4032733 0.023567375279699945 0.1897921323965865 chr7 159138663 3844178 0.024156153680894 0.24182889099270913 chr8 146364022 3497810 0.023898017779259987 0.21250247964296248 chr9 141213431 2952349 0.020906998570128926 0.17589096391794545 chr10 135534747 3402212 0.02510213856820052 0.25048327838734946 chr11 135006516 3128452 0.023172600054355896 0.18673139646078019 chr12 133851895 3178013 0.02374275687318435 0.16762513881368948 chr13 115169878 2156180 0.01872173555658364 0.14696692982631349 chr14 107349540 2132840 0.019868180152425433 0.15910581016866918 chr15 102531392 1993170 0.019439607335088167 0.15326265971912495 chr16 90354753 2080900 0.02303033244969415 0.17417999250640487 chr17 81195210 2013349 0.024796401167014655 0.17631052158726687 chr18 78077248 1782300 0.02282739268679142 0.26726641597099143 chr19 59128983 1543040 0.026096170130306486 0.23268457994623704 chr20 63025520 1499553 0.023792790602917675 0.17108212618543966 chr21 48129895 906129 0.0188267395970841 0.16385891815653794 chr22 51304566 847530 0.016519582292149202 0.13878953593898358 chrMT 16571 17633 1.0640878643413192 1.2734836505676244 chrX 155270560 3904747 0.025148019044949666 0.18146691092179285 chrY 59373566 234668 0.003952398614561908 0.12911700660715333