BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008810.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,272,724 number of mapped reads = 1,100,452 (86.46%) number of supplementary alignments = 5,568 (0.44%) number of secondary alignments = 0 number of mapped bases = 71,683,418 bp number of sequenced bases = 71,644,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,640 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1571 >>>>>>> ACTG content number of A's = 20,105,430 bp (28.06%) number of C's = 13,037,318 bp (18.2%) number of T's = 22,294,639 bp (31.12%) number of G's = 16,193,203 bp (22.6%) number of N's = 14,308 bp (0.02%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 565,735 number of insertions = 6,402 mapped reads with insertion percentage = 0.58% number of deletions = 23,154 mapped reads with deletion percentage = 2.08% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2823X There is a 2.12% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 6106983 0.024501375264376974 0.5622324666650709 chr2 243199373 4823838 0.019834911334249205 0.27326458609424964 chr3 198022430 5926536 0.029928609602457662 0.1920018741890705 chr4 191154276 2859748 0.014960418672507227 0.13582416258696026 chr5 180915260 4272102 0.0236138289274216 0.16372800133941928 chr6 171115067 3690241 0.02156584492936557 0.17036857203713376 chr7 159138663 3842594 0.02414620009720705 0.3988055655493363 chr8 146364022 5536846 0.03782928293675887 0.310092328731368 chr9 141213431 2117073 0.014992008798369894 0.2215526716173083 chr10 135534747 3647432 0.026911416302713872 0.3648199534861216 chr11 135006516 3859292 0.028585968398740103 0.2944990547044401 chr12 133851895 3776935 0.02821726954257913 0.18074103461688545 chr13 115169878 2054110 0.01783547951661458 0.1398238820661778 chr14 107349540 3080333 0.028694421978892503 0.1842199040878516 chr15 102531392 1822748 0.017777462730633756 0.1410210537848779 chr16 90354753 2095833 0.02319560322410488 0.19389991431218648 chr17 81195210 1838625 0.022644500827080808 0.20280116298191472 chr18 78077248 715080 0.009158621984217477 0.42254065030462307 chr19 59128983 1479526 0.025022009933774778 0.3638523519024948 chr20 63025520 1616672 0.025651069598473762 0.1721970970533065 chr21 48129895 755991 0.015707306238669335 0.1476596038615705 chr22 51304566 640742 0.012488985873109228 0.11690965436059803 chrMT 16571 40898 2.4680465874117434 2.0297519158808837 chrX 155270560 4871345 0.03137326869948817 0.22289630726448473 chrY 59373566 211895 0.0035688440879565833 0.0955374763173906