BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716187.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 = 1,955,576 number of mapped reads = 1,702,626 (87.07%) number of supplementary alignments = 6,594 (0.34%) number of secondary alignments = 0 number of mapped bases = 96,292,045 bp number of sequenced bases = 96,262,905 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,365 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.738 >>>>>>> ACTG content number of A's = 24,140,945 bp (25.08%) number of C's = 18,712,859 bp (19.44%) number of T's = 30,254,693 bp (31.43%) number of G's = 23,153,541 bp (24.05%) number of N's = 867 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 513,182 number of insertions = 7,064 mapped reads with insertion percentage = 0.41% number of deletions = 18,272 mapped reads with deletion percentage = 1.06% homopolymer indels = 40.85% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2645X There is a 2.8% of reference with a coverageData >= 1X There is a 0.22% 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 0.01% 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 8088286 0.03245041463708129 0.3509499397348223 chr2 243199373 7551120 0.031049093206338158 0.40165739752812435 chr3 198022430 5559276 0.028073971216291002 0.1871574345637148 chr4 191154276 5896943 0.030849129422561284 0.21014673124145247 chr5 180915260 5456727 0.030161784030821943 0.18894036466331865 chr6 171115067 5124892 0.02994997512404913 0.22339239298286634 chr7 159138663 5493209 0.034518380992053455 0.369281812136078 chr8 146364022 4951195 0.033827951243373185 0.2587873887723894 chr9 141213431 3195005 0.022625362030896337 0.19566184958225377 chr10 135534747 4310136 0.031800966876781786 0.3333696062966109 chr11 135006516 3401781 0.025197161594778136 0.22133483199728962 chr12 133851895 4754745 0.035522433208734175 0.2063579611846333 chr13 115169878 2883734 0.025038960273970248 0.1718190937994849 chr14 107349540 3210610 0.02990799960577381 0.20073585211874606 chr15 102531392 3561728 0.03473792689754958 0.20975116408785222 chr16 90354753 3354693 0.037128019153569045 0.22635128704405783 chr17 81195210 4342105 0.0534773541444132 0.26691984421521275 chr18 78077248 1780968 0.02281033265926586 0.310206108349494 chr19 59128983 2632232 0.04451678122047186 0.32310048883264375 chr20 63025520 3102155 0.0492206172991512 0.2558411690634792 chr21 48129895 1219261 0.02533271680729825 0.18866184119052426 chr22 51304566 907818 0.01769468237973205 0.1451916674093758 chrMT 16571 52095 3.143745096855953 2.7642096891369112 chrX 155270560 5153503 0.0331904708787036 0.2113996550164141 chrY 59373566 307828 0.005184596795146177 0.14873276114756337