BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068935.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 = 2,177,259 number of mapped reads = 1,846,347 (84.8%) number of supplementary alignments = 8,955 (0.41%) number of secondary alignments = 0 number of mapped bases = 118,760,487 bp number of sequenced bases = 118,706,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,888 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1773 >>>>>>> ACTG content number of A's = 30,996,850 bp (26.11%) number of C's = 20,494,246 bp (17.26%) number of T's = 39,141,320 bp (32.97%) number of G's = 27,791,112 bp (23.41%) number of N's = 283,084 bp (0.24%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,100,058 number of insertions = 10,695 mapped reads with insertion percentage = 0.57% number of deletions = 33,059 mapped reads with deletion percentage = 1.77% homopolymer indels = 48.5% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3579X There is a 3.38% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 17537121 0.07035938738945008 0.6159494333765639 chr2 243199373 3373355 0.013870738885498689 0.24518216193096742 chr3 198022430 6958040 0.035137635670868195 0.2608636866202718 chr4 191154276 6305768 0.03298784694724799 0.21164583391751968 chr5 180915260 5886683 0.03253834419495625 0.19891581559591406 chr6 171115067 7332830 0.0428532105825608 0.26412008803074843 chr7 159138663 5465890 0.034346713092593975 0.271672097940895 chr8 146364022 6828370 0.046653336705929 0.43777583119099783 chr9 141213431 6890721 0.04879649868432132 0.3546799195773666 chr10 135534747 9771088 0.07209286338948934 0.77005130238848 chr11 135006516 6018013 0.044575722552532206 0.44039380939593165 chr12 133851895 4413699 0.03297449767147488 0.2078258518163862 chr13 115169878 2527917 0.021949463209468712 0.1603588130796964 chr14 107349540 3567524 0.03323278329837277 0.23183534524383925 chr15 102531392 2698128 0.026315140635172495 0.17778976779531042 chr16 90354753 2440148 0.027006304803909982 0.22053375587619853 chr17 81195210 3239531 0.03989805556263725 0.2579478317607178 chr18 78077248 1803015 0.023092706853602218 0.5124919094931669 chr19 59128983 2351225 0.03976434027285739 0.4172759773849037 chr20 63025520 1236713 0.019622416443370875 0.1674515339207782 chr21 48129895 1633395 0.0339372234242356 0.22073166639658756 chr22 51304566 1053156 0.020527529654962875 0.15837988780469653 chrMT 16571 64433 3.8882988353147065 3.1330706032513596 chrX 155270560 9066322 0.05839047659775298 0.32365049783797945 chrY 59373566 297402 0.005008996764654493 0.11123122018455713