BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013309.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,242,803 number of mapped reads = 2,779,537 (85.71%) number of supplementary alignments = 19,399 (0.6%) number of secondary alignments = 0 number of mapped bases = 181,260,050 bp number of sequenced bases = 181,153,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,401 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7543 >>>>>>> ACTG content number of A's = 49,806,901 bp (27.49%) number of C's = 34,314,151 bp (18.94%) number of T's = 55,868,883 bp (30.84%) number of G's = 41,122,702 bp (22.7%) number of N's = 40,998 bp (0.02%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,563,095 number of insertions = 12,700 mapped reads with insertion percentage = 0.45% number of deletions = 60,808 mapped reads with deletion percentage = 2.16% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.4976X There is a 4.97% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14272477 0.05726155041354942 0.8955924330690637 chr2 243199373 19414701 0.07983039084562113 0.603343802198797 chr3 198022430 9440485 0.0476738165469437 0.24703264995281887 chr4 191154276 12877364 0.0673663402643423 0.3208448356805055 chr5 180915260 8556791 0.04729723186424407 0.24751220816949004 chr6 171115067 7970324 0.04657873873841863 0.3736070212293301 chr7 159138663 13377080 0.08405927100191862 0.9021470159772734 chr8 146364022 13730457 0.09381032860657519 0.5409042217118677 chr9 141213431 5848856 0.041418553168643 0.39017962985631677 chr10 135534747 6626289 0.04888996472616723 0.5531350232474009 chr11 135006516 9102227 0.0674206495336862 0.393191027564958 chr12 133851895 11747597 0.08776563828252114 0.34026257638505947 chr13 115169878 3939058 0.03420215483774325 0.21318014666728866 chr14 107349540 4408482 0.041066612861126374 0.26140461117679964 chr15 102531392 3973795 0.038756861898451546 0.22148865198865433 chr16 90354753 6801280 0.07527307390237678 0.3554679931441721 chr17 81195210 4906551 0.06042906964585719 0.35067780150832545 chr18 78077248 5078726 0.06504745146755173 0.6586028625058669 chr19 59128983 3128587 0.05291122629320379 0.780009163195783 chr20 63025520 3422959 0.05431068240293773 0.27130305152125717 chr21 48129895 1737832 0.036107122195051536 0.24822565126282845 chr22 51304566 1877181 0.036588965590314125 0.21433818799399829 chrMT 16571 143508 8.660189487659164 5.510191970521888 chrX 155270560 8490593 0.054682568285964836 0.3210725329905496 chrY 59373566 386850 0.006515525781287922 0.1809425778620397