BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525161.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 = 909,222 number of mapped reads = 364,730 (40.11%) number of supplementary alignments = 1,182 (0.13%) number of secondary alignments = 0 number of mapped bases = 22,911,821 bp number of sequenced bases = 22,903,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,962 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0241 >>>>>>> ACTG content number of A's = 6,100,443 bp (26.64%) number of C's = 4,671,239 bp (20.4%) number of T's = 6,788,270 bp (29.64%) number of G's = 5,343,358 bp (23.33%) number of N's = 527 bp (0%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 108,971 number of insertions = 1,705 mapped reads with insertion percentage = 0.47% number of deletions = 4,996 mapped reads with deletion percentage = 1.36% homopolymer indels = 44.14% >>>>>>> Coverage mean coverageData = 0.0074X std coverageData = 0.1062X There is a 0.71% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2338743 0.009383097986343633 0.17091916385619235 chr2 243199373 1850396 0.0076085558000184485 0.10497422372583866 chr3 198022430 1692608 0.008547556961097791 0.09501556607181243 chr4 191154276 1185356 0.006201043601033544 0.08110169027386299 chr5 180915260 973954 0.005383481747200319 0.07499486524016301 chr6 171115067 1296176 0.007574879423096039 0.09149831431154119 chr7 159138663 1638823 0.010298081994065766 0.16147177927028442 chr8 146364022 1426215 0.00974430041284326 0.10581689823312057 chr9 141213431 730738 0.005174706080188647 0.0824373203239442 chr10 135534747 1518576 0.011204329764971635 0.12315885794498238 chr11 135006516 1004767 0.007442359300642941 0.09694078499291428 chr12 133851895 1013039 0.007568357549215123 0.08902761948773599 chr13 115169878 657693 0.005710633816943003 0.07717528406789859 chr14 107349540 684251 0.006374046875282372 0.08342003010062678 chr15 102531392 616527 0.006013055981918201 0.07950090272623543 chr16 90354753 648007 0.007171808659584294 0.09003453211515884 chr17 81195210 403016 0.004963544031723053 0.07311704804754875 chr18 78077248 488903 0.006261785763760526 0.13647823819205857 chr19 59128983 446221 0.007546569843760039 0.13682579515042315 chr20 63025520 415943 0.0065995964809175715 0.08324520882499054 chr21 48129895 362240 0.007526299402897098 0.08990953675698223 chr22 51304566 262711 0.005120616359955175 0.07309706354448174 chrMT 16571 4214 0.2542996801641422 0.5188139286590654 chrX 155270560 1188353 0.00765343410882269 0.09081449015254985 chrY 59373566 64351 0.0010838324920554713 0.03989241210058409