BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716545.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 = 982,939 number of mapped reads = 932,845 (94.9%) number of supplementary alignments = 19,940 (2.03%) number of secondary alignments = 0 number of mapped bases = 72,953,073 bp number of sequenced bases = 72,925,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,822 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4426 >>>>>>> ACTG content number of A's = 18,682,976 bp (25.62%) number of C's = 15,421,276 bp (21.15%) number of T's = 21,323,609 bp (29.24%) number of G's = 17,494,925 bp (23.99%) number of N's = 2,676 bp (0%) GC percentage = 45.14% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 456,140 number of insertions = 6,644 mapped reads with insertion percentage = 0.7% number of deletions = 13,034 mapped reads with deletion percentage = 1.37% homopolymer indels = 36.54% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.2325X There is a 2.08% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 8201231 0.032903552926353594 0.42116711561839104 chr2 243199373 6993456 0.028756060978824976 0.23792815292494426 chr3 198022430 4872490 0.02460574794481615 0.17488075541882475 chr4 191154276 3558483 0.018615764577508066 0.20043173591523827 chr5 180915260 3772321 0.02085131458783521 0.15928935503368813 chr6 171115067 4483717 0.02620293512785756 0.18618932824171291 chr7 159138663 4698790 0.029526388568439838 0.3010312454219276 chr8 146364022 4530287 0.030952189876279842 0.25344512712805284 chr9 141213431 2236475 0.015837551599465066 0.16339648590764294 chr10 135534747 3872549 0.028572370449033265 0.328194104989116 chr11 135006516 2251975 0.016680491184588454 0.18181579081149918 chr12 133851895 2686584 0.02007131837767407 0.15609894554293466 chr13 115169878 1402571 0.012178279810281644 0.12036271980082107 chr14 107349540 1472922 0.013720804020212848 0.13617770278899516 chr15 102531392 1464598 0.014284386190719034 0.13021373538620465 chr16 90354753 2290152 0.02534622611386033 0.18644564163931565 chr17 81195210 1811146 0.02230606953291949 0.17783950933271336 chr18 78077248 2227948 0.028535175829967778 0.2574567557165745 chr19 59128983 1273870 0.02154391865660872 0.3043945996611526 chr20 63025520 1430274 0.02269356920815568 0.17266487294177504 chr21 48129895 1142874 0.023745615900471008 0.19615846604762957 chr22 51304566 1184027 0.02307839423103199 0.1717062365517408 chrMT 16571 27078 1.6340595015388328 1.684883241583107 chrX 155270560 4813239 0.030999044506569692 0.2026440712478548 chrY 59373566 254016 0.004278267537442504 0.16355984125270406