BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716589.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 = 453,007 number of mapped reads = 386,095 (85.23%) number of supplementary alignments = 1,013 (0.22%) number of secondary alignments = 0 number of mapped bases = 22,096,131 bp number of sequenced bases = 22,089,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,195 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4446 >>>>>>> ACTG content number of A's = 5,536,804 bp (25.07%) number of C's = 4,042,937 bp (18.3%) number of T's = 7,177,163 bp (32.49%) number of G's = 5,332,291 bp (24.14%) number of N's = 279 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 112,762 number of insertions = 1,354 mapped reads with insertion percentage = 0.35% number of deletions = 4,222 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.61% >>>>>>> Coverage mean coverageData = 0.0071X std coverageData = 0.0987X There is a 0.68% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2600644 0.010433851637224205 0.1259972147916178 chr2 243199373 2280784 0.009378247862505797 0.13241289782672108 chr3 198022430 1441998 0.007281993257026489 0.08795490434624834 chr4 191154276 952699 0.004983927223265463 0.07348875094492824 chr5 180915260 1633271 0.009027823302467685 0.09751477181419228 chr6 171115067 845944 0.004943714278532819 0.07584861414684298 chr7 159138663 1314650 0.008261034592203405 0.13683695929260611 chr8 146364022 991364 0.006773276563826594 0.08941920199235957 chr9 141213431 629804 0.004459944040308744 0.07842019248956547 chr10 135534747 1024259 0.007557169085208829 0.10444638728424267 chr11 135006516 948040 0.0070221795813173934 0.09394146486019891 chr12 133851895 840554 0.006279731788631009 0.08147866767252296 chr13 115169878 644468 0.0055958034443693684 0.07693618885570827 chr14 107349540 492122 0.004584295377511632 0.07038501176868708 chr15 102531392 964705 0.009408874503527662 0.09979397006720185 chr16 90354753 729009 0.008068297192954531 0.0946544339005114 chr17 81195210 830791 0.010232019844520384 0.10656515865977774 chr18 78077248 601006 0.007697581759029212 0.12849039863631048 chr19 59128983 361582 0.006115139846054852 0.10389051746752072 chr20 63025520 551223 0.008746028592862066 0.09644377360240038 chr21 48129895 274266 0.0056984541520400155 0.07815006740338398 chr22 51304566 240222 0.004682273308773336 0.07004362247693788 chrMT 16571 7444 0.44921851427192083 0.6800704143666012 chrX 155270560 848180 0.005462593810442881 0.0805585884483821 chrY 59373566 47102 7.933160019393142E-4 0.03242382147345921