BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716487.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 = 1,483,987 number of mapped reads = 607,915 (40.96%) number of supplementary alignments = 2,847 (0.19%) number of secondary alignments = 0 number of mapped bases = 34,919,185 bp number of sequenced bases = 34,908,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,866 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6371 >>>>>>> ACTG content number of A's = 8,604,249 bp (24.65%) number of C's = 7,171,707 bp (20.54%) number of T's = 11,122,346 bp (31.86%) number of G's = 8,010,162 bp (22.95%) number of N's = 415 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 175,934 number of insertions = 2,902 mapped reads with insertion percentage = 0.47% number of deletions = 6,625 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0113X std coverageData = 0.1331X There is a 1.06% of reference with a coverageData >= 1X There is a 0.05% 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 2858918 0.01147005366939487 0.20605219200091662 chr2 243199373 2909519 0.01196351357369659 0.16504078598202881 chr3 198022430 2301867 0.011624274078446567 0.11276771341389136 chr4 191154276 2212253 0.011573128502759728 0.11623678987784072 chr5 180915260 2091051 0.011558179227114397 0.11249697014836654 chr6 171115067 2020897 0.011810163975799981 0.12154312506704566 chr7 159138663 1913841 0.012026247826400301 0.15028911229980665 chr8 146364022 1742358 0.011904277951585671 0.1243670446549606 chr9 141213431 1456824 0.010316469118295129 0.11869522423545507 chr10 135534747 1696972 0.012520567880648347 0.1360659954260042 chr11 135006516 1596607 0.01182614770978906 0.1258303525725509 chr12 133851895 1607099 0.012006546489311936 0.11509689079551844 chr13 115169878 1076353 0.009345785709697461 0.10068106038093766 chr14 107349540 1054035 0.009818719297725915 0.10517128553546842 chr15 102531392 1019129 0.009939677791558707 0.10476482092983117 chr16 90354753 1038468 0.011493230466802338 0.11554923773782638 chr17 81195210 977946 0.01204438045052165 0.11783216329343357 chr18 78077248 900670 0.01153562687045527 0.15560870146832062 chr19 59128983 757644 0.012813411656344571 0.15534186291991442 chr20 63025520 751743 0.011927596948029941 0.11483339493848335 chr21 48129895 450595 0.009362060731692849 0.10400663287914627 chr22 51304566 428406 0.008350250930882059 0.09658277068790391 chrMT 16571 3561 0.2148934886247058 0.49374607256931663 chrX 155270560 1944106 0.012520763755859449 0.12136449123739088 chrY 59373566 108323 0.0018244314313208003 0.061118266747979585