BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236095.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,111,307 number of mapped reads = 923,728 (83.12%) number of supplementary alignments = 4,917 (0.44%) number of secondary alignments = 0 number of mapped bases = 60,886,979 bp number of sequenced bases = 60,857,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,382 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5304 >>>>>>> ACTG content number of A's = 16,920,023 bp (27.8%) number of C's = 10,790,825 bp (17.73%) number of T's = 19,331,161 bp (31.76%) number of G's = 13,781,735 bp (22.65%) number of N's = 33,583 bp (0.06%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 523,365 number of insertions = 5,132 mapped reads with insertion percentage = 0.55% number of deletions = 16,830 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2375X There is a 1.8% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4698635 0.018851046312939778 0.28029900554535375 chr2 243199373 5154805 0.021195798888840062 0.28024068994706125 chr3 198022430 5575023 0.028153492510924142 0.1779888012218737 chr4 191154276 3110416 0.016271757373609575 0.15737808970691136 chr5 180915260 3989638 0.022052523374755672 0.15965343945489974 chr6 171115067 5035417 0.029427081368585736 0.2534679253048479 chr7 159138663 2739068 0.017211832425662644 0.24622188282412483 chr8 146364022 3766112 0.025731132204060366 0.5050986942224375 chr9 141213431 2960899 0.0209675452188397 0.26599800223961256 chr10 135534747 2046379 0.015098556239604004 0.2221889109206235 chr11 135006516 2445256 0.018112133195111856 0.19608348010181742 chr12 133851895 2276819 0.017009987045756805 0.14560064922080185 chr13 115169878 2541398 0.02206651638547364 0.15688523342872662 chr14 107349540 1666619 0.015525162008146472 0.15889750049124038 chr15 102531392 1475945 0.014395054736016849 0.13277457898031875 chr16 90354753 2235604 0.024742516865714857 0.1842955136410297 chr17 81195210 1027002 0.012648554021844392 0.13239294150948816 chr18 78077248 1555172 0.019918376221456986 0.4203195161099665 chr19 59128983 823225 0.013922529328806483 0.2401229689601624 chr20 63025520 928153 0.014726621850958152 0.13577091343980344 chr21 48129895 935382 0.019434532321335834 0.1786980501473999 chr22 51304566 296033 0.005770110208124556 0.07911189634452163 chrMT 16571 26236 1.5832478426166194 1.6503783845462328 chrX 155270560 3413364 0.021983330259129612 0.17560421302389853 chrY 59373566 164379 0.0027685552860341922 0.09691462314042391