BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716678.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 = 3,480,719 number of mapped reads = 3,124,558 (89.77%) number of supplementary alignments = 20,137 (0.58%) number of secondary alignments = 0 number of mapped bases = 182,605,042 bp number of sequenced bases = 182,553,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,719 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6773 >>>>>>> ACTG content number of A's = 43,937,163 bp (24.07%) number of C's = 33,837,907 bp (18.54%) number of T's = 58,681,627 bp (32.14%) number of G's = 46,095,427 bp (25.25%) number of N's = 1,370 bp (0%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 903,453 number of insertions = 13,037 mapped reads with insertion percentage = 0.42% number of deletions = 32,728 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.059X std coverageData = 0.4688X There is a 4.7% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% 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 21332223 0.08558543571291644 0.7769891771902498 chr2 243199373 18516119 0.07613555401723836 0.6761671590421388 chr3 198022430 11354493 0.05733942866977241 0.29165136265190045 chr4 191154276 7500014 0.039235397485955274 0.28839449902927067 chr5 180915260 12870110 0.07113888568603886 0.32615967521694195 chr6 171115067 6684014 0.03906151642391608 0.2810678872711352 chr7 159138663 12126532 0.07620104235763248 0.7915177911663118 chr8 146364022 8068993 0.05512962058394378 0.40775139111279535 chr9 141213431 4981096 0.03527352862065932 0.34174521480965225 chr10 135534747 8101651 0.059775453743976074 0.38435036259263405 chr11 135006516 8903385 0.0659478169187034 0.46538606081599804 chr12 133851895 7644295 0.05711009918836039 0.29335568989738603 chr13 115169878 5183553 0.04500788826050506 0.25862720768437214 chr14 107349540 3834420 0.03571901658824062 0.24579884560355406 chr15 102531392 7880231 0.07685676402403666 0.3416702655932792 chr16 90354753 5375138 0.059489266712953105 0.3181518568269043 chr17 81195210 6930946 0.08536151332079811 0.4069446545830749 chr18 78077248 5767487 0.07386898421419771 0.7940236111287519 chr19 59128983 2893993 0.048943730353014865 0.5566059644982191 chr20 63025520 4789798 0.07599775456037491 0.3428068660433507 chr21 48129895 2301548 0.04781951009866113 0.2912688950824633 chr22 51304566 2201269 0.04290590821877335 0.2505960556491845 chrMT 16571 235857 14.233118097881842 10.054485311813336 chrX 155270560 6708334 0.04320415924306578 0.2936918203141257 chrY 59373566 419543 0.007066158027294504 0.16502844199666641