BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238044.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 = 2,874,908 number of mapped reads = 2,077,984 (72.28%) number of supplementary alignments = 18,832 (0.66%) number of secondary alignments = 0 number of mapped bases = 135,033,894 bp number of sequenced bases = 134,968,536 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 352,014 duplication rate = 12.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2426 >>>>>>> ACTG content number of A's = 38,552,330 bp (28.56%) number of C's = 25,286,508 bp (18.74%) number of T's = 42,008,754 bp (31.12%) number of G's = 28,858,437 bp (21.38%) number of N's = 262,507 bp (0.19%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,292,002 number of insertions = 13,105 mapped reads with insertion percentage = 0.62% number of deletions = 39,269 mapped reads with deletion percentage = 1.87% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.6578X There is a 1.49% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 9916581 0.039785581918369624 0.8082806172052047 chr2 243199373 12579846 0.05172647381784163 0.8527067223563517 chr3 198022430 8088481 0.04084628695850263 0.5015762612955545 chr4 191154276 9120771 0.0477141876752995 0.604034834366613 chr5 180915260 8226272 0.04547030471614169 0.535396513535584 chr6 171115067 6672338 0.038993281637788216 0.5196259900289015 chr7 159138663 5990996 0.03764638892309909 0.6054209128687807 chr8 146364022 6451884 0.044081078886995875 0.7339951869746831 chr9 141213431 6286792 0.04451978792300571 0.6955883129273694 chr10 135534747 5640841 0.04161915025377219 0.749143607440259 chr11 135006516 6128300 0.04539262386416964 0.5948027769491248 chr12 133851895 6035505 0.04509091933289402 0.5349598490305214 chr13 115169878 3950154 0.03429849947396836 0.45104143443409317 chr14 107349540 3564765 0.03320708221013336 0.48379497455587833 chr15 102531392 3291038 0.03209785740546661 0.455143468767514 chr16 90354753 4747978 0.052548181942348955 0.6129669324901943 chr17 81195210 4060184 0.05000521582492366 0.6479293576608817 chr18 78077248 6776669 0.08679441416787641 1.2887556878882165 chr19 59128983 2359493 0.03990417017657821 0.7408834528501508 chr20 63025520 2758423 0.04376676305090382 0.5296151438694732 chr21 48129895 1826150 0.037942114770871616 0.5309375374037755 chr22 51304566 3200024 0.062373083908360126 0.6385946180507207 chrMT 16571 195708 11.810270955283327 9.388902161260628 chrX 155270560 6553588 0.042207537604037754 0.5517022900294194 chrY 59373566 611113 0.010292678058110911 0.43453618788221066