BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524623.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 = 2,105,460 number of mapped reads = 1,962,314 (93.2%) number of supplementary alignments = 4,287 (0.2%) number of secondary alignments = 0 number of mapped bases = 114,592,248 bp number of sequenced bases = 114,554,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,875 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4579 >>>>>>> ACTG content number of A's = 29,458,519 bp (25.72%) number of C's = 21,184,384 bp (18.49%) number of T's = 34,911,195 bp (30.48%) number of G's = 28,999,792 bp (25.32%) number of N's = 788 bp (0%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 534,435 number of insertions = 6,651 mapped reads with insertion percentage = 0.34% number of deletions = 21,707 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3138X There is a 3.18% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11747329 0.04713059069971184 0.5520741556127635 chr2 243199373 10142810 0.04170574074629707 0.36553447420376245 chr3 198022430 7251384 0.036619003210898886 0.21733179068282107 chr4 191154276 5109167 0.026727976516727252 0.2188817815262173 chr5 180915260 7071979 0.039090008217106724 0.2243274416034118 chr6 171115067 7454526 0.043564404530198386 0.25721708532815796 chr7 159138663 6915071 0.04345311736092693 0.4173855532209723 chr8 146364022 10237580 0.06994601446522151 0.40796803379288404 chr9 141213431 4103905 0.02906171864062987 0.27584979507100743 chr10 135534747 4943388 0.0364732152412547 0.3226424760879749 chr11 135006516 5795350 0.0429264466020292 0.299689719452325 chr12 133851895 3495896 0.02611764293662036 0.19069188028279663 chr13 115169878 2813459 0.0244287746836026 0.17861081115586513 chr14 107349540 2104669 0.019605757043765628 0.1698340656614875 chr15 102531392 2900523 0.02828912144292355 0.2021824276252023 chr16 90354753 3382626 0.03743716725117936 0.23615366666445242 chr17 81195210 2520512 0.031042619386045064 0.208576114650917 chr18 78077248 3059794 0.03918931671362187 0.4508166029602349 chr19 59128983 2243799 0.03794753243092309 0.39891819190867484 chr20 63025520 2121425 0.033659777816985884 0.21715437634602522 chr21 48129895 1660355 0.03449737424110316 0.2296505543104186 chr22 51304566 2057690 0.04010734639096255 0.22809561099311518 chrMT 16571 10724 0.6471546677931326 0.9377167427502977 chrX 155270560 5161769 0.033243706984762596 0.2426450313816138 chrY 59373566 286518 0.00482568286365013 0.13187669699517793