BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236107.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 = 1,211,033 number of mapped reads = 1,054,676 (87.09%) number of supplementary alignments = 6,467 (0.53%) number of secondary alignments = 0 number of mapped bases = 69,950,449 bp number of sequenced bases = 69,915,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,495 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3717 >>>>>>> ACTG content number of A's = 19,442,867 bp (27.81%) number of C's = 12,358,327 bp (17.68%) number of T's = 22,781,432 bp (32.58%) number of G's = 15,292,055 bp (21.87%) number of N's = 40,357 bp (0.06%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 574,718 number of insertions = 5,139 mapped reads with insertion percentage = 0.48% number of deletions = 20,372 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2446X There is a 2% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 5673246 0.022761211094434946 0.31168799939311137 chr2 243199373 4845417 0.01992364100379486 0.2354696975596566 chr3 198022430 5584326 0.028200472037435354 0.18387045396552923 chr4 191154276 3394504 0.017757928679555147 0.15466032453812598 chr5 180915260 3381728 0.018692331426326335 0.1502545190971298 chr6 171115067 7722186 0.04512861512072458 0.3087883848285552 chr7 159138663 4910685 0.030857900320552523 0.4111589479100642 chr8 146364022 4275967 0.029214604392328054 0.4624395650910481 chr9 141213431 2468779 0.017482607585676463 0.20651225112856145 chr10 135534747 2876174 0.021220934584398495 0.2166444822526049 chr11 135006516 1958849 0.01450929227741867 0.16849938736716333 chr12 133851895 2489735 0.018600670539628893 0.15516628760069232 chr13 115169878 3337531 0.02897920062049558 0.18758445534931392 chr14 107349540 1785053 0.01662841778362534 0.14908397992651293 chr15 102531392 1937315 0.018894847345874325 0.1514485240729098 chr16 90354753 2957090 0.032727553358482424 0.20858752030763472 chr17 81195210 1710447 0.021065860904848945 0.1790361331513738 chr18 78077248 1610963 0.020632937779774204 0.3689080318204794 chr19 59128983 860970 0.014560879560536328 0.24350678915292534 chr20 63025520 867625 0.013766248973431715 0.1340038487280578 chr21 48129895 1333857 0.0277136902127046 0.1891729278576293 chr22 51304566 711339 0.013865023241790994 0.1277617792331968 chrMT 16571 10495 0.633335344879609 0.8782872558702144 chrX 155270560 3088380 0.01989031275471667 0.16928437197739943 chrY 59373566 157788 0.0026575462892021676 0.0792050493912139