BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524534.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 = 1,710,685 number of mapped reads = 1,568,161 (91.67%) number of supplementary alignments = 6,099 (0.36%) number of secondary alignments = 0 number of mapped bases = 91,482,703 bp number of sequenced bases = 91,453,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,804 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0972 >>>>>>> ACTG content number of A's = 23,232,587 bp (25.4%) number of C's = 17,993,591 bp (19.68%) number of T's = 28,508,263 bp (31.17%) number of G's = 21,718,201 bp (23.75%) number of N's = 1,271 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 468,415 number of insertions = 7,297 mapped reads with insertion percentage = 0.46% number of deletions = 17,420 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2765X There is a 2.6% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 9087871 0.036460775758709145 0.49674634932242717 chr2 243199373 7183776 0.029538628785856287 0.32376346554231233 chr3 198022430 4975501 0.025125946590999818 0.175976288296916 chr4 191154276 5085557 0.026604463715998693 0.2163761077613668 chr5 180915260 4959352 0.02741256873521891 0.1852184191011575 chr6 171115067 3920917 0.022913920256946163 0.20816471020233193 chr7 159138663 4539633 0.02852627334188424 0.3433644012383192 chr8 146364022 8331251 0.056921440707607775 0.3157479862360718 chr9 141213431 3919111 0.027753103739827693 0.23395700009244969 chr10 135534747 4802161 0.03543121676391959 0.2806780563249455 chr11 135006516 3146494 0.02330623804853982 0.25832584375679324 chr12 133851895 4213339 0.031477619349356244 0.19801648447555079 chr13 115169878 2026738 0.017597813205984292 0.14810279241454014 chr14 107349540 2169483 0.0202095230217102 0.16162722929027004 chr15 102531392 2464029 0.024031947210860063 0.17594980763574936 chr16 90354753 2885148 0.031931336251895905 0.21171929776312712 chr17 81195210 3254433 0.04008158855676339 0.23433030804445437 chr18 78077248 2147821 0.027508922957940322 0.4167556056318769 chr19 59128983 1930547 0.03264975824123341 0.3629620907223814 chr20 63025520 2666444 0.04230737009389213 0.23143407783551992 chr21 48129895 1262355 0.026228085475773426 0.2055015885689277 chr22 51304566 767349 0.014956738938206787 0.1352506610019875 chrMT 16571 24592 1.4840383803029389 1.5187050577095578 chrX 155270560 5398092 0.03476571476266976 0.22708099568698076 chrY 59373566 320709 0.005401545192687264 0.17989138567046084