BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524378.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 = 973,817 number of mapped reads = 897,377 (92.15%) number of supplementary alignments = 2,987 (0.31%) number of secondary alignments = 0 number of mapped bases = 52,261,158 bp number of sequenced bases = 52,244,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,805 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7028 >>>>>>> ACTG content number of A's = 12,682,407 bp (24.28%) number of C's = 9,982,231 bp (19.11%) number of T's = 16,584,142 bp (31.74%) number of G's = 12,994,422 bp (24.87%) number of N's = 1,109 bp (0%) GC percentage = 43.98% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 259,743 number of insertions = 3,166 mapped reads with insertion percentage = 0.35% number of deletions = 10,580 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1864X There is a 1.56% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4164606 0.016708508020126456 0.3056482388336721 chr2 243199373 4446617 0.01828383414458885 0.2509478780707468 chr3 198022430 3488789 0.017618150630713904 0.14174630682956518 chr4 191154276 3418195 0.01788186522178557 0.14885991569548956 chr5 180915260 3156136 0.017445382993120647 0.14062791411583886 chr6 171115067 3022990 0.01766641624843007 0.14896438429640615 chr7 159138663 2878052 0.018085183988255576 0.2434679695380766 chr8 146364022 2643882 0.0180637424680773 0.1980893945209624 chr9 141213431 2195231 0.015545483063859555 0.1590149225207277 chr10 135534747 2532877 0.018688026916079313 0.18277590806445593 chr11 135006516 2346168 0.017378183435235083 0.16082440563928796 chr12 133851895 2360698 0.017636642350113908 0.142009413890595 chr13 115169878 1609621 0.013976058913598918 0.1259100206144547 chr14 107349540 1583961 0.014755172681690113 0.13121842175590603 chr15 102531392 1481908 0.014453212534167098 0.12731072881319308 chr16 90354753 1504141 0.016647060061134804 0.14660852279110695 chr17 81195210 1398104 0.01721904531067781 0.1417682663314431 chr18 78077248 1397057 0.017893266422505057 0.2502725971696797 chr19 59128983 1073725 0.01815903040307661 0.2285856074987224 chr20 63025520 1081439 0.017158747758051023 0.1403024118269702 chr21 48129895 689902 0.014334167984368136 0.1345407439566624 chr22 51304566 596808 0.011632648836752659 0.11428035743050657 chrMT 16571 6070 0.36630257679077904 0.6189924665824531 chrX 155270560 3021717 0.019460978307800268 0.15626216762893408 chrY 59373566 162464 0.0027363018754844536 0.08890834450263475