BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716284.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,774,918 number of mapped reads = 1,622,782 (91.43%) number of supplementary alignments = 6,813 (0.38%) number of secondary alignments = 0 number of mapped bases = 93,448,117 bp number of sequenced bases = 93,423,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,951 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.884 >>>>>>> ACTG content number of A's = 23,719,295 bp (25.39%) number of C's = 18,831,253 bp (20.16%) number of T's = 28,541,903 bp (30.55%) number of G's = 22,329,105 bp (23.9%) number of N's = 2,073 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 453,173 number of insertions = 7,026 mapped reads with insertion percentage = 0.43% number of deletions = 14,535 mapped reads with deletion percentage = 0.89% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.2365X There is a 2.71% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 10503894 0.0421418970105595 0.34966280552671025 chr2 243199373 7955390 0.03271139189984672 0.26800065775361237 chr3 198022430 6167046 0.031143168983432837 0.19314145303943592 chr4 191154276 5924771 0.030994708169646175 0.20485888370515873 chr5 180915260 4798858 0.02652544622272328 0.18019675015532968 chr6 171115067 4971826 0.02905545424588473 0.19890561534102244 chr7 159138663 4082447 0.025653395114925655 0.21265297800858507 chr8 146364022 6005479 0.04103111487329857 0.2501654875692347 chr9 141213431 3427376 0.024270892476226286 0.25004615211907427 chr10 135534747 4415486 0.03257825832662675 0.23921908443932138 chr11 135006516 3926737 0.029085536878827388 0.24374658979461936 chr12 133851895 4235287 0.031641591626326994 0.19669555254008808 chr13 115169878 2910131 0.025268160829344632 0.173309345632274 chr14 107349540 2540267 0.02366351080777803 0.17600063078413974 chr15 102531392 2710319 0.026434040805766102 0.17765971949271106 chr16 90354753 2757404 0.030517531269218343 0.20648807979354297 chr17 81195210 2161393 0.0266197106947565 0.18650712640667144 chr18 78077248 2311081 0.029599929034384 0.44215167409322764 chr19 59128983 1766414 0.02987391141159996 0.28928351101956395 chr20 63025520 2017986 0.03201855375409834 0.20229681838605593 chr21 48129895 1211562 0.025172753857036257 0.18613541475975506 chr22 51304566 1154046 0.02249402129237386 0.16401547734848052 chrMT 16571 6125 0.3696216281455555 0.6822201230600514 chrX 155270560 5242781 0.03376545431406958 0.22416172522514372 chrY 59373566 244011 0.004109758204518152 0.09715156797647773