BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,257,458 number of mapped reads = 2,138,362 (94.72%) number of supplementary alignments = 36,186 (1.6%) number of secondary alignments = 0 number of mapped bases = 197,785,304 bp number of sequenced bases = 197,665,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,069,659 duplication rate = 42.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0572 >>>>>>> ACTG content number of A's = 56,958,017 bp (28.82%) number of C's = 41,165,749 bp (20.83%) number of T's = 57,419,557 bp (29.05%) number of G's = 42,112,300 bp (21.3%) number of N's = 9,783 bp (0%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,226,020 number of insertions = 30,548 mapped reads with insertion percentage = 1.39% number of deletions = 64,110 mapped reads with deletion percentage = 2.94% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.773X There is a 2.64% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 20221933 0.08113092324050819 1.3336491746565065 chr2 243199373 16984466 0.069837622484331 1.1599718939930124 chr3 198022430 11149513 0.05630429340757004 0.4671296280233095 chr4 191154276 10916225 0.05710688365663345 0.5423759176305686 chr5 180915260 11010382 0.060859332706373136 0.4975450552239706 chr6 171115067 7545981 0.044098869446721485 0.47826871319739683 chr7 159138663 9501753 0.05970738235999884 0.9124612891958924 chr8 146364022 18476133 0.12623411646886828 0.7731967117440685 chr9 141213431 8206786 0.05811618584637321 0.6769788517087795 chr10 135534747 10125691 0.07470918878094043 0.8931121589728134 chr11 135006516 6789912 0.050293216958505915 0.5224898605019693 chr12 133851895 9472468 0.07076827713197487 0.532031120396966 chr13 115169878 4010309 0.034820814866192706 0.36320107395792145 chr14 107349540 4737889 0.044135158846512056 0.4400915370468746 chr15 102531392 5318605 0.05187294248380047 0.45260322482498294 chr16 90354753 5485014 0.06070531784863603 0.8469926834966938 chr17 81195210 6932492 0.08538055385286891 0.630474345838555 chr18 78077248 4972290 0.06368423743623751 0.8557241974222694 chr19 59128983 3772205 0.0637962097200285 1.136428435460616 chr20 63025520 5557269 0.0881749012146191 0.6204772109628128 chr21 48129895 2856842 0.05935691320332197 0.5113846132281854 chr22 51304566 1612945 0.031438624780492246 0.3860362674278543 chrMT 16571 11297 0.681733148271076 1.849699492826793 chrX 155270560 11393318 0.07337719397675901 0.6226007061746855 chrY 59373566 723586 0.012187005914382841 0.7662094260624148