BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004099.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 = 3,007,006 number of mapped reads = 2,562,874 (85.23%) number of supplementary alignments = 22,991 (0.76%) number of secondary alignments = 0 number of mapped bases = 172,791,093 bp number of sequenced bases = 172,716,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,450 duplication rate = 5.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4529 >>>>>>> ACTG content number of A's = 48,087,100 bp (27.84%) number of C's = 31,854,723 bp (18.44%) number of T's = 56,052,656 bp (32.45%) number of G's = 36,698,732 bp (21.25%) number of N's = 23,339 bp (0.01%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,648,252 number of insertions = 13,697 mapped reads with insertion percentage = 0.53% number of deletions = 45,292 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 0.5036X There is a 3.97% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15380167 0.061705631618065256 0.9636226966125411 chr2 243199373 13911851 0.05720348218167487 0.5337535674919145 chr3 198022430 11322358 0.05717714907346607 0.3196324661746849 chr4 191154276 12533459 0.06556724370633488 0.34995504490422463 chr5 180915260 10918097 0.06034923201061093 0.32647716723314685 chr6 171115067 10920507 0.06381966936903341 0.39577759904046345 chr7 159138663 9865709 0.06199441929457457 0.6405128095163796 chr8 146364022 8724814 0.05961037337440754 0.6632859815973926 chr9 141213431 7439807 0.05268483987192408 0.4586186367904603 chr10 135534747 8166639 0.06025494702107645 0.5109947680088571 chr11 135006516 7165083 0.053072127274212455 0.4234712160095857 chr12 133851895 8057934 0.06020037295699101 0.33270256325369296 chr13 115169878 5554991 0.04823301974844499 0.2891936376964891 chr14 107349540 4815721 0.04486019222811761 0.30784676145850337 chr15 102531392 5222632 0.05093690720594138 0.30088757457313503 chr16 90354753 4461471 0.04937726961635322 0.32494272352736553 chr17 81195210 3983126 0.049056169692768825 0.33659498676256533 chr18 78077248 4458744 0.05710682835542564 0.8270989378230535 chr19 59128983 2411148 0.040777768831234594 0.6177633352319613 chr20 63025520 4045739 0.06419207647949593 0.3477440098573122 chr21 48129895 2149970 0.044670157705517535 0.3039644254861951 chr22 51304566 1428701 0.027847443441973565 0.2141876559099177 chrMT 16571 85257 5.144952024621326 3.90647298157714 chrX 155270560 9348082 0.0602051155093406 0.36207655420645135 chrY 59373566 419086 0.007058460999293861 0.15186339592594367