BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524398.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 = 1,022,390 number of mapped reads = 949,739 (92.89%) number of supplementary alignments = 4,154 (0.41%) number of secondary alignments = 0 number of mapped bases = 55,634,092 bp number of sequenced bases = 55,617,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,497 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7168 >>>>>>> ACTG content number of A's = 13,323,697 bp (23.96%) number of C's = 11,361,938 bp (20.43%) number of T's = 17,767,529 bp (31.95%) number of G's = 13,157,275 bp (23.66%) number of N's = 7,284 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 270,455 number of insertions = 4,125 mapped reads with insertion percentage = 0.43% number of deletions = 10,231 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.1983X There is a 1.66% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4687273 0.018805461672249956 0.391186155600279 chr2 243199373 4562736 0.01876129836897236 0.20933715617236068 chr3 198022430 3846293 0.01942352187072949 0.1467851401201824 chr4 191154276 3589615 0.018778627792767764 0.15617394014436398 chr5 180915260 3443736 0.019035077527456777 0.1457128353647959 chr6 171115067 1992920 0.011646665807634578 0.11966143550016174 chr7 159138663 3191999 0.02005797296411872 0.2617440159248505 chr8 146364022 2991321 0.020437543045926956 0.17906931170616613 chr9 141213431 2073458 0.014683150075151138 0.15222501500498578 chr10 135534747 2793964 0.0206143742607938 0.18440713387225935 chr11 135006516 2278492 0.016876903926622326 0.16890365770118332 chr12 133851895 2551648 0.019063219090024838 0.15052673510968037 chr13 115169878 1814542 0.015755352280567667 0.13271516303813702 chr14 107349540 1608863 0.01498714386666212 0.13263601406568343 chr15 102531392 1710033 0.016678140876113336 0.13647897779689389 chr16 90354753 1689889 0.018702823524956124 0.1483573714862086 chr17 81195210 1485119 0.018290721829526645 0.15062687890296633 chr18 78077248 1595061 0.02042926769140224 0.2582597563740718 chr19 59128983 1562058 0.026417805968352272 0.2769731381639043 chr20 63025520 1614313 0.025613640315859353 0.17359643608467742 chr21 48129895 779323 0.016192077709706203 0.14316814349475337 chr22 51304566 381329 0.007432652290636276 0.090663045493678 chrMT 16571 8472 0.5112546014121054 0.7856603246484257 chrX 155270560 3212306 0.020688442161862493 0.1642355003308114 chrY 59373566 169329 0.0028519257206144565 0.08323609484564966