BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716224.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 = 1,419,047 number of mapped reads = 1,271,221 (89.58%) number of supplementary alignments = 5,120 (0.36%) number of secondary alignments = 0 number of mapped bases = 73,089,411 bp number of sequenced bases = 73,069,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,312 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1875 >>>>>>> ACTG content number of A's = 19,110,628 bp (26.15%) number of C's = 12,348,075 bp (16.9%) number of T's = 23,333,462 bp (31.93%) number of G's = 18,276,246 bp (25.01%) number of N's = 1,099 bp (0%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 391,393 number of insertions = 5,164 mapped reads with insertion percentage = 0.4% number of deletions = 11,866 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.2241X There is a 2.15% 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 5872018 0.023558689548861745 0.3819636140883109 chr2 243199373 6321662 0.025993743001960782 0.2477101161486469 chr3 198022430 4993758 0.02521814321741229 0.1701060881387848 chr4 191154276 4599901 0.024063814298352394 0.18226096891486196 chr5 180915260 4425822 0.024463508495634917 0.1686345709367231 chr6 171115067 4194032 0.024510009980593935 0.17783737835353117 chr7 159138663 4018227 0.025249847675294344 0.23696308574557032 chr8 146364022 3768600 0.025748130917036427 0.2429434614933826 chr9 141213431 3119692 0.022092034574246695 0.21874325702131073 chr10 135534747 3252065 0.023994326709445218 0.237042242416748 chr11 135006516 3401289 0.02519351732623039 0.21170335075516866 chr12 133851895 3349206 0.02502173017423474 0.17377843645065574 chr13 115169878 2273861 0.01974353919173206 0.15023210328584458 chr14 107349540 2239396 0.020860788038775016 0.16428886833648032 chr15 102531392 2071565 0.02020420243587447 0.152450741935686 chr16 90354753 2004841 0.022188550501598958 0.17507622250902835 chr17 81195210 1884102 0.023204595443499683 0.1699825230291869 chr18 78077248 2051622 0.026276822666700547 0.37104136813565053 chr19 59128983 1459685 0.024686455371640673 0.2881145707406519 chr20 63025520 1593868 0.02528924791100494 0.17673871842893452 chr21 48129895 963731 0.02002354254045225 0.16742976598560372 chr22 51304566 832940 0.01623520214555562 0.13587293590704302 chrMT 16571 10626 0.6412407217428037 0.8936636552914673 chrX 155270560 4166826 0.02683590501637915 0.19430408090932605 chrY 59373566 220076 0.003706632678926511 0.10451399012726564