BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524797.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 = 1,330,669 number of mapped reads = 1,205,485 (90.59%) number of supplementary alignments = 4,314 (0.32%) number of secondary alignments = 0 number of mapped bases = 68,717,772 bp number of sequenced bases = 68,696,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,437 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.419 >>>>>>> ACTG content number of A's = 17,015,718 bp (24.77%) number of C's = 12,641,678 bp (18.4%) number of T's = 22,356,858 bp (32.54%) number of G's = 16,673,789 bp (24.27%) number of N's = 8,037 bp (0.01%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 353,940 number of insertions = 4,675 mapped reads with insertion percentage = 0.39% number of deletions = 13,616 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.12% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.2099X There is a 2.01% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 5503097 0.02207856886342522 0.2855296317970979 chr2 243199373 5814220 0.02390721624105503 0.33061788552708343 chr3 198022430 4485918 0.022653585252943316 0.1647303131122106 chr4 191154276 4401721 0.023027060090458035 0.18400912842941658 chr5 180915260 4077107 0.02253600387275236 0.1621929779692104 chr6 171115067 3846672 0.02248003093731074 0.1740292740946739 chr7 159138663 3751309 0.0235725808504499 0.2430507571995465 chr8 146364022 3438310 0.02349149711122314 0.18870019567130286 chr9 141213431 2924738 0.020711471842929728 0.18056998541993424 chr10 135534747 3327824 0.024553290382428646 0.24201414866964188 chr11 135006516 3121031 0.02311763233709401 0.18936616515041083 chr12 133851895 3113235 0.023258804068481808 0.16710431899110176 chr13 115169878 2159026 0.01874644687910497 0.14820391133289915 chr14 107349540 2096487 0.019529538738591708 0.1540573205140258 chr15 102531392 2012146 0.019624682360695932 0.1549116327928911 chr16 90354753 2094495 0.023180794927301723 0.17902361441042822 chr17 81195210 1960624 0.024147040201016785 0.17290572009193736 chr18 78077248 1782997 0.02283631974323685 0.2737127844350232 chr19 59128983 1512254 0.025575511758759658 0.23678410545057937 chr20 63025520 1489775 0.02363764709914333 0.1699365995164157 chr21 48129895 902149 0.018744046709430803 0.1645270037392768 chr22 51304566 851136 0.016589868433932373 0.1398658782117523 chrMT 16571 8297 0.5006939834650896 0.8040369747901168 chrX 155270560 3812883 0.02455638081037384 0.18027229227592892 chrY 59373566 230321 0.003879184214739603 0.11274456971155818