BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524539.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 = 2,546,533 number of mapped reads = 2,335,634 (91.72%) number of supplementary alignments = 8,761 (0.34%) number of secondary alignments = 0 number of mapped bases = 136,360,317 bp number of sequenced bases = 136,316,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,350 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1184 >>>>>>> ACTG content number of A's = 35,765,186 bp (26.24%) number of C's = 27,960,237 bp (20.51%) number of T's = 41,426,490 bp (30.39%) number of G's = 31,162,895 bp (22.86%) number of N's = 2,177 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 691,541 number of insertions = 9,998 mapped reads with insertion percentage = 0.43% number of deletions = 25,887 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.3927X There is a 3.7% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13439692 0.05392039524748065 0.755639483017194 chr2 243199373 10746504 0.044188041553873576 0.4595714142287921 chr3 198022430 7388446 0.03731115712497821 0.2248770996535514 chr4 191154276 7550589 0.03949997435579207 0.27911847228397185 chr5 180915260 7471389 0.041297726902639394 0.2368678968120038 chr6 171115067 5837817 0.03411632360813674 0.2815508337402376 chr7 159138663 6750526 0.04241914486864829 0.5020836059263832 chr8 146364022 12430492 0.08492860356078491 0.4311825168638742 chr9 141213431 5844861 0.0413902626585144 0.32655653895401127 chr10 135534747 7128328 0.0525940997255855 0.38476262713077136 chr11 135006516 4635758 0.03433729080157879 0.35835059953064297 chr12 133851895 6295821 0.04703572556817369 0.2521819723827754 chr13 115169878 3024811 0.026263907303956682 0.1910659453065979 chr14 107349540 3231012 0.030098051654436526 0.20517675877727592 chr15 102531392 3611694 0.03522525081879314 0.22430464063367997 chr16 90354753 4216985 0.04667142413637056 0.26870112172893945 chr17 81195210 4866844 0.05994003833477369 0.3079395359978243 chr18 78077248 3251933 0.04165020006852701 0.6119557337915917 chr19 59128983 2841747 0.048060136600015596 0.48881870081637846 chr20 63025520 3944838 0.0625911218185903 0.294685129503836 chr21 48129895 1890767 0.039284669123005565 0.2632565485951181 chr22 51304566 1157137 0.022554269341251224 0.17298147199695 chrMT 16571 274765 16.58107537263895 10.938020046746155 chrX 155270560 8062394 0.051924807896616076 0.30455321036700167 chrY 59373566 465167 0.007834580796443993 0.2419174288505686