BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716657.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 = 1,641,950 number of mapped reads = 1,518,922 (92.51%) number of supplementary alignments = 9,286 (0.57%) number of secondary alignments = 0 number of mapped bases = 88,955,070 bp number of sequenced bases = 88,928,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,574 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6369 >>>>>>> ACTG content number of A's = 21,357,641 bp (24.02%) number of C's = 17,961,610 bp (20.2%) number of T's = 27,166,470 bp (30.55%) number of G's = 22,441,516 bp (25.24%) number of N's = 1,103 bp (0%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 441,211 number of insertions = 5,032 mapped reads with insertion percentage = 0.33% number of deletions = 16,679 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.81% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2561X There is a 2.59% 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 7422382 0.029778790400686705 0.40036415904393147 chr2 243199373 8699875 0.035772604561772454 0.3268633372427204 chr3 198022430 6057426 0.030589595330185574 0.19180428018261308 chr4 191154276 4934701 0.02581527917272434 0.19262225977288405 chr5 180915260 4785490 0.02645155527510504 0.17611938226918442 chr6 171115067 4983409 0.029123145538084032 0.19670456030939557 chr7 159138663 4352559 0.027350732486674217 0.3864910949563755 chr8 146364022 6978075 0.04767616320355012 0.3157564087634974 chr9 141213431 3765075 0.02666230098183791 0.19850938626527262 chr10 135534747 4184323 0.030872695693304388 0.3055343284756581 chr11 135006516 3071762 0.02275269439587642 0.20244797450708787 chr12 133851895 4114642 0.030740259598117756 0.1988746079740309 chr13 115169878 2293405 0.019913236341189838 0.1520072848515674 chr14 107349540 2867397 0.026710845710191212 0.1800471994484207 chr15 102531392 2144266 0.020913263325245793 0.1571987470461012 chr16 90354753 2739692 0.030321503950102104 0.19607038992257034 chr17 81195210 3853047 0.0474541170593684 0.2459283608829845 chr18 78077248 2055183 0.026322431343891627 0.3094103259920526 chr19 59128983 1865675 0.031552631304346976 0.3438446836324657 chr20 63025520 2064843 0.03276201449825404 0.20135890466461864 chr21 48129895 906875 0.01884223931924223 0.15949568140779016 chr22 51304566 1393920 0.027169511579144826 0.17940297825542975 chrMT 16571 93884 5.665560316215075 3.7994806139797133 chrX 155270560 3121854 0.020105897731031563 0.17089797776872873 chrY 59373566 205310 0.0034579361461967773 0.10052982843506