BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238260.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 = 2,114,247 number of mapped reads = 1,877,345 (88.79%) number of supplementary alignments = 23,801 (1.13%) number of secondary alignments = 0 number of mapped bases = 121,773,428 bp number of sequenced bases = 121,718,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,411 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6438 >>>>>>> ACTG content number of A's = 34,405,289 bp (28.27%) number of C's = 22,919,536 bp (18.83%) number of T's = 37,862,324 bp (31.11%) number of G's = 26,498,594 bp (21.77%) number of N's = 32,629 bp (0.03%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,046,610 number of insertions = 9,605 mapped reads with insertion percentage = 0.51% number of deletions = 33,669 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.339X There is a 3.06% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7309432 0.029325632051283836 0.5453642966629113 chr2 243199373 7984797 0.032832309152375984 0.37626133164920317 chr3 198022430 14011195 0.07075559571711144 0.32767001511898664 chr4 191154276 12402128 0.06488020179051605 0.3206556181889181 chr5 180915260 6294399 0.034791973877714905 0.23063251651299305 chr6 171115067 10576661 0.06181022621462083 0.34469595680937765 chr7 159138663 5186105 0.03258859225177731 0.35024180381889114 chr8 146364022 7502628 0.05126005624524311 0.5000290608447587 chr9 141213431 3787450 0.02682074908299622 0.28340811573800145 chr10 135534747 5338903 0.039391396805425846 0.332084605347618 chr11 135006516 3879895 0.028738575847702046 0.25863012928783075 chr12 133851895 4173308 0.031178549993632888 0.22106625912846867 chr13 115169878 3007928 0.026117315154228087 0.200854360720007 chr14 107349540 3218516 0.02998164687058743 0.23836525605163197 chr15 102531392 4853161 0.047333415701602884 0.27628457519334565 chr16 90354753 3838246 0.04247973540473294 0.28020897252596555 chr17 81195210 2441957 0.030075136205694894 0.23151948183463214 chr18 78077248 4184429 0.05359344888795261 0.5068928566427334 chr19 59128983 1678620 0.028389123486192887 0.3915851270209846 chr20 63025520 2180762 0.034601253587435696 0.23317843442607253 chr21 48129895 1259863 0.026176308924006585 0.21084470288084095 chr22 51304566 968288 0.018873329909856365 0.16709439115917593 chrMT 16571 23876 1.4408303663025768 1.655984135316914 chrX 155270560 5367173 0.03456658493406606 0.2503588817518448 chrY 59373566 303708 0.005115205645556138 0.16930219277885705