BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,273,844 number of mapped reads = 3,214,190 (98.18%) number of supplementary alignments = 388,636 (11.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,605,119 number of mapped paired reads (second in pair) = 1,609,071 number of mapped paired reads (both in pair) = 3,176,746 number of mapped paired reads (singletons) = 37,444 number of mapped bases = 369,537,293 bp number of sequenced bases = 369,318,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,574,507 duplication rate = 65.82% >>>>>>> Insert size mean insert size = 1,021,468.5713 std insert size = 9,530,858.9229 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.6851 >>>>>>> ACTG content number of A's = 110,402,857 bp (29.89%) number of C's = 73,530,619 bp (19.91%) number of T's = 109,389,670 bp (29.62%) number of G's = 75,991,986 bp (20.58%) number of N's = 2,914 bp (0%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 3,042,508 number of insertions = 40,285 mapped reads with insertion percentage = 1.2% number of deletions = 90,449 mapped reads with deletion percentage = 2.74% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.1194X std coverageData = 2.1506X There is a 2.54% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 1.45% of reference with a coverageData >= 3X There is a 1.17% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 30404596 0.12198403309093461 1.1900025991906438 chr2 243199373 34967787 0.1437823896034469 6.509805537239108 chr3 198022430 28096052 0.14188317959738198 1.1448132740898735 chr4 191154276 24509768 0.1282198259587978 1.3162910095970972 chr5 180915260 20972050 0.1159219515258138 1.0200461931055023 chr6 171115067 21646542 0.1265028403372568 1.1160678818719676 chr7 159138663 23422836 0.14718507469174855 1.5201127952680735 chr8 146364022 20390379 0.1393127813883114 1.5055686097772831 chr9 141213431 15815966 0.11200043712555925 1.3208133726107376 chr10 135534747 18399575 0.13575540890632273 1.5542096689862968 chr11 135006516 15487676 0.11471798887099642 1.0366674834909992 chr12 133851895 15908414 0.11885086871575483 1.0540350068343751 chr13 115169878 10769638 0.09351089179759312 0.9224573876427207 chr14 107349540 11678545 0.1087898932776051 1.0038528745419923 chr15 102531392 10522868 0.10263069480223189 0.9595635553655257 chr16 90354753 11568711 0.1280365516576643 1.189818485248335 chr17 81195210 10043031 0.1236899442713431 1.1375950518197842 chr18 78077248 9010548 0.11540555322851544 1.4849760560369536 chr19 59128983 7146691 0.12086612414761133 1.159972517086035 chr20 63025520 8025532 0.12733781490418483 1.0994198551130427 chr21 48129895 4844493 0.10065455160456926 1.111602626996481 chr22 51304566 4402032 0.08580195376762373 0.9375967194063928 chrMT 16571 396738 23.941705388932473 29.060471016409252 chrX 155270560 8699688 0.05602921764434932 0.709159299810926 chrY 59373566 2407137 0.04054223389580474 0.719988625633215