BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716567.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 = 1,025,467 number of mapped reads = 939,011 (91.57%) number of supplementary alignments = 20,995 (2.05%) number of secondary alignments = 0 number of mapped bases = 72,433,578 bp number of sequenced bases = 72,404,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,978 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8619 >>>>>>> ACTG content number of A's = 18,127,368 bp (25.04%) number of C's = 14,253,093 bp (19.69%) number of T's = 22,171,760 bp (30.62%) number of G's = 17,849,291 bp (24.65%) number of N's = 2,958 bp (0%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 481,072 number of insertions = 6,194 mapped reads with insertion percentage = 0.65% number of deletions = 13,803 mapped reads with deletion percentage = 1.45% homopolymer indels = 39.13% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.2056X There is a 2.1% of reference with a coverageData >= 1X There is a 0.18% 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 5862913 0.023522160051107757 0.2904388417584953 chr2 243199373 6105445 0.025104690545398732 0.22239229196011165 chr3 198022430 4752627 0.02400044782805665 0.16800724458501387 chr4 191154276 4608399 0.02410827053641217 0.22051064056131342 chr5 180915260 4317708 0.023865913798537502 0.16809703304493553 chr6 171115067 4078379 0.023834131450271412 0.17274818744869755 chr7 159138663 3881569 0.02439111229682758 0.21547882569320828 chr8 146364022 3666664 0.02505167560918762 0.2079596620835387 chr9 141213431 3036310 0.02150156666046872 0.18656176004477204 chr10 135534747 3499358 0.025818899414775165 0.26086768556707607 chr11 135006516 3345595 0.024780989089445135 0.21434676810354927 chr12 133851895 3260680 0.024360357393520653 0.17132200059363675 chr13 115169878 2202628 0.01912503545414887 0.1503166904024071 chr14 107349540 2188171 0.020383608537120887 0.16444375836716676 chr15 102531392 2082819 0.020313963941892058 0.15503431995477193 chr16 90354753 2246372 0.024861691559269716 0.18136653432706784 chr17 81195210 2017174 0.024843509857293306 0.18554893761425836 chr18 78077248 1917879 0.02456386526328387 0.27501264048764096 chr19 59128983 1519244 0.02569372789652073 0.2268862486888543 chr20 63025520 1595986 0.025322853345755816 0.1830185684759536 chr21 48129895 998219 0.020740103422207758 0.19125750097928626 chr22 51304566 961540 0.018741801655626517 0.15354028806561965 chrMT 16571 4504 0.27180013276205417 0.5519214029656564 chrX 155270560 4033151 0.02597498843309382 0.18403070334239752 chrY 59373566 250244 0.004214737582041139 0.16398289494315238