BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063551.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 = 2,709,303 number of mapped reads = 2,374,719 (87.65%) number of supplementary alignments = 12,352 (0.46%) number of secondary alignments = 0 number of mapped bases = 149,554,603 bp number of sequenced bases = 149,493,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,162 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1128 >>>>>>> ACTG content number of A's = 38,289,784 bp (25.61%) number of C's = 27,002,221 bp (18.06%) number of T's = 47,125,961 bp (31.52%) number of G's = 37,072,473 bp (24.8%) number of N's = 2,667 bp (0%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,206,749 number of insertions = 11,355 mapped reads with insertion percentage = 0.47% number of deletions = 38,638 mapped reads with deletion percentage = 1.61% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.4839X There is a 4.05% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15167851 0.06085381428197124 0.89556240650335 chr2 243199373 12235849 0.05031200882248985 0.8884729399028386 chr3 198022430 11860137 0.05989289698141771 0.2858574983381474 chr4 191154276 8529507 0.044621063041247376 0.26815230885797303 chr5 180915260 6658717 0.03680572329829999 0.22615483920759388 chr6 171115067 9059678 0.0529449461045999 0.3336900006801917 chr7 159138663 9210890 0.05787964927165437 0.5265748918713415 chr8 146364022 5071196 0.034647831691862085 0.45215006249446343 chr9 141213431 5048302 0.03574944652396414 0.4336602619083252 chr10 135534747 9194160 0.06783618373523065 0.4024051813703229 chr11 135006516 6143802 0.045507447951623314 0.3366865015911394 chr12 133851895 6829267 0.05102107071401567 0.28111311718193294 chr13 115169878 3716246 0.03226751703253519 0.21154682290236046 chr14 107349540 3551321 0.03308184646156844 0.2604233707270249 chr15 102531392 2973689 0.02900271752869599 0.24141941349391077 chr16 90354753 2643639 0.029258438678925944 0.23802255110086049 chr17 81195210 5429648 0.06687153096839087 0.32227138243795656 chr18 78077248 3936235 0.05041462270801348 0.6480079787564573 chr19 59128983 4353050 0.07361956487565498 0.6681719684744528 chr20 63025520 2444348 0.03878346422211193 0.24252889761435856 chr21 48129895 2383976 0.049532125511597316 0.27583409571296064 chr22 51304566 2162107 0.0421425843461964 0.23836256712457277 chrMT 16571 17746 1.070907006215678 1.3692414311517702 chrX 155270560 10458539 0.06735687048465594 0.38328102136807224 chrY 59373566 474703 0.007995190991223266 0.16268458426560709