BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716139.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 = 440,427 number of mapped reads = 403,763 (91.68%) number of supplementary alignments = 1,159 (0.26%) number of secondary alignments = 0 number of mapped bases = 23,361,372 bp number of sequenced bases = 23,354,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,495 duplication rate = 1.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6033 >>>>>>> ACTG content number of A's = 5,512,834 bp (23.61%) number of C's = 4,352,516 bp (18.64%) number of T's = 7,526,047 bp (32.23%) number of G's = 5,962,790 bp (25.53%) number of N's = 145 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 113,927 number of insertions = 1,361 mapped reads with insertion percentage = 0.33% number of deletions = 4,308 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0075X std coverageData = 0.0997X There is a 0.72% 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 2842805 0.011405407892644728 0.13459598817533677 chr2 243199373 2403978 0.009884803444785198 0.12587355912881223 chr3 198022430 1495754 0.0075534574542893956 0.08991469311325273 chr4 191154276 993459 0.005197158132104772 0.0756901993887293 chr5 180915260 1643030 0.009081765684110893 0.09792145214669952 chr6 171115067 903240 0.005278553290692981 0.07850130657959195 chr7 159138663 1289638 0.008103863484136473 0.11635270759850676 chr8 146364022 1072630 0.007328508641283443 0.09317334436616585 chr9 141213431 642402 0.004549156517555331 0.07993275406311791 chr10 135534747 1010525 0.007455837136730701 0.10992978603118003 chr11 135006516 1044457 0.007736345110927831 0.09787188182027526 chr12 133851895 851950 0.00636487066544706 0.08246148060284847 chr13 115169878 717219 0.006227487711674054 0.08100043529229788 chr14 107349540 515232 0.004799573430868917 0.07212653952178746 chr15 102531392 1033286 0.01007775257747403 0.10341739001136865 chr16 90354753 737128 0.008158154115035874 0.09656489602083203 chr17 81195210 894643 0.01101842091423866 0.11110272650177888 chr18 78077248 773885 0.009911786337551241 0.13742079957566924 chr19 59128983 383412 0.0064843327340840615 0.10532288572040965 chr20 63025520 587137 0.009315861257471577 0.09983594196356418 chr21 48129895 308097 0.0064013644742004945 0.08337724343967735 chr22 51304566 269459 0.005252144614185022 0.07448696467505769 chrMT 16571 2784 0.16800434493995534 0.40926538351958 chrX 155270560 891948 0.005744475965050941 0.08137971107517349 chrY 59373566 53274 8.9726798622808E-4 0.03478414347293282