BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234078.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 = 3,811,888 number of mapped reads = 3,611,082 (94.73%) number of supplementary alignments = 35,446 (0.93%) number of secondary alignments = 0 number of mapped bases = 233,575,094 bp number of sequenced bases = 233,488,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 461,506 duplication rate = 10.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0089 >>>>>>> ACTG content number of A's = 59,655,831 bp (25.55%) number of C's = 43,149,289 bp (18.48%) number of T's = 74,866,717 bp (32.06%) number of G's = 55,793,304 bp (23.9%) number of N's = 23,043 bp (0.01%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,242,589 number of insertions = 14,663 mapped reads with insertion percentage = 0.4% number of deletions = 50,096 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0755X std coverageData = 0.7157X There is a 5.49% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20206852 0.08107041787470612 1.1746166654480048 chr2 243199373 18717807 0.076964865365833 1.5327733117455875 chr3 198022430 25029474 0.12639716622000852 0.47142201018689833 chr4 191154276 6307521 0.03299701755036858 0.2710234671320087 chr5 180915260 10972275 0.0606486981805736 0.3297986367017702 chr6 171115067 13008313 0.07602085092834052 0.5333185843233192 chr7 159138663 15015433 0.09435439959678435 0.8155031453157263 chr8 146364022 8514669 0.058174603865422614 0.7638971740629926 chr9 141213431 8629724 0.06111121257297403 0.44861513337763764 chr10 135534747 11105633 0.08193937898449023 0.5104582469411013 chr11 135006516 10469573 0.07754864957777297 0.47736162169850654 chr12 133851895 9364651 0.06996278237226301 0.3480813834273266 chr13 115169878 5695142 0.04944992648164479 0.35513507496266833 chr14 107349540 11401968 0.10621347795249053 0.4379561600907385 chr15 102531392 8412311 0.08204619908018024 0.3890082082537316 chr16 90354753 4488995 0.04968189111202595 0.3332275980893603 chr17 81195210 8366030 0.10303600421749017 0.4412674964386942 chr18 78077248 3781482 0.048432572828386575 1.0261544927308086 chr19 59128983 9554264 0.1615834319355704 0.710737474772173 chr20 63025520 7810595 0.12392749794051679 0.47778038409667334 chr21 48129895 4096565 0.08511477118327393 0.3957899948805886 chr22 51304566 3562514 0.0694385369130693 0.3415906506334993 chrMT 16571 165778 10.004103554402269 6.883838671062099 chrX 155270560 8407579 0.05414792733406771 0.34394746339716037 chrY 59373566 489946 0.00825192140219437 0.2082389213252943