BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716372.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 = 2,545,004 number of mapped reads = 2,377,339 (93.41%) number of supplementary alignments = 46,524 (1.83%) number of secondary alignments = 0 number of mapped bases = 188,753,850 bp number of sequenced bases = 188,664,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,759 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.528 >>>>>>> ACTG content number of A's = 49,272,004 bp (26.12%) number of C's = 37,636,372 bp (19.95%) number of T's = 57,324,658 bp (30.38%) number of G's = 44,417,829 bp (23.54%) number of N's = 13,647 bp (0.01%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,245,253 number of insertions = 15,990 mapped reads with insertion percentage = 0.66% number of deletions = 47,107 mapped reads with deletion percentage = 1.95% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.061X std coverageData = 0.5436X There is a 5.01% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 18444709 0.07400065414480954 1.1767244550616096 chr2 243199373 15319739 0.06299251026440764 0.578063546360268 chr3 198022430 11975953 0.060477760019407904 0.2853172966661437 chr4 191154276 11938033 0.06245234608301412 0.39078676562989184 chr5 180915260 10882814 0.06015420700277025 0.28621497406441065 chr6 171115067 10318854 0.060303596760418535 0.3142055198965056 chr7 159138663 9829888 0.06176932628873475 0.6380209957463961 chr8 146364022 9221604 0.0630045818227105 0.587107105220216 chr9 141213431 7689814 0.05445525928762399 0.44039669133779125 chr10 135534747 8827754 0.06513277366430617 0.5440684019804995 chr11 135006516 10560204 0.07821995791669789 0.586874496375028 chr12 133851895 8076280 0.06033743489399235 0.2872538383397268 chr13 115169878 6545674 0.0568349477629906 0.27913599729918864 chr14 107349540 5514860 0.05137292623703837 0.28685607584313366 chr15 102531392 5301340 0.05170455503032671 0.2628011465891996 chr16 90354753 4193883 0.04641574306555849 0.28559384954715705 chr17 81195210 5978561 0.07363194208131243 0.39632091707594125 chr18 78077248 4938261 0.06324839984114194 0.7944617707128191 chr19 59128983 3739924 0.06325026763947555 0.7663373831081248 chr20 63025520 3858010 0.06121345765969087 0.3068518115506125 chr21 48129895 2507857 0.05210601435968227 0.33041658847960803 chr22 51304566 2214671 0.043167132531634705 0.24251735716369308 chrMT 16571 68822 4.153159133425865 2.927869519783087 chrX 155270560 10224475 0.06584941150466643 0.3640743878837278 chrY 59373566 581866 0.009800085108581822 0.3288820062285454