BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231862.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 = 873,133 number of mapped reads = 607,201 (69.54%) number of supplementary alignments = 4,368 (0.5%) number of secondary alignments = 0 number of mapped bases = 40,681,448 bp number of sequenced bases = 40,654,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,940 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3132 >>>>>>> ACTG content number of A's = 11,668,299 bp (28.7%) number of C's = 7,140,574 bp (17.56%) number of T's = 13,305,071 bp (32.73%) number of G's = 8,538,044 bp (21%) number of N's = 2,183 bp (0.01%) GC percentage = 38.57% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 336,908 number of insertions = 3,346 mapped reads with insertion percentage = 0.54% number of deletions = 15,576 mapped reads with deletion percentage = 2.52% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1822X There is a 1.19% of reference with a coverageData >= 1X There is a 0.09% 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 4833225 0.019391024907416378 0.3700581612978999 chr2 243199373 1549681 0.0063720600134935385 0.11943552146486619 chr3 198022430 4766764 0.024071838730592286 0.16720170716081525 chr4 191154276 1415079 0.007402811119956322 0.09356808781150593 chr5 180915260 2698589 0.014916314964254536 0.13212133934602735 chr6 171115067 4645156 0.027146387991654763 0.1964217043650849 chr7 159138663 2609344 0.01639666911113863 0.19638310795831224 chr8 146364022 3158829 0.02158200462679278 0.3501051036661808 chr9 141213431 1574114 0.011147055834936834 0.12520358346044586 chr10 135534747 1291429 0.009528397909651907 0.14342483066875283 chr11 135006516 794646 0.005885982569907959 0.09660167820630107 chr12 133851895 885885 0.00661839714708559 0.08854961939453311 chr13 115169878 1892109 0.016428853037423554 0.13902532026814757 chr14 107349540 1379387 0.012849491483615114 0.12461796669087391 chr15 102531392 603525 0.005886246038676623 0.08233559076584138 chr16 90354753 1152778 0.012758354837182722 0.1264965707287799 chr17 81195210 179948 0.0022162391106568973 0.05279584772862745 chr18 78077248 587582 0.007525649469612454 0.1903630271335073 chr19 59128983 1229624 0.0207956223431071 0.24179280123513652 chr20 63025520 551319 0.00874755178537202 0.1015089521853814 chr21 48129895 356510 0.00740724657720529 0.09326320668442409 chr22 51304566 245653 0.004788131333183873 0.0737023177778932 chrMT 16571 10799 0.6516806469132822 0.9320987115070141 chrX 155270560 2177942 0.014026754331278254 0.13061551897179072 chrY 59373566 91531 0.0015416119692052857 0.044907220364319975