BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716958.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 = 976,518 number of mapped reads = 897,956 (91.95%) number of supplementary alignments = 2,930 (0.3%) number of secondary alignments = 0 number of mapped bases = 52,070,434 bp number of sequenced bases = 52,054,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,094 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4256 >>>>>>> ACTG content number of A's = 13,283,348 bp (25.52%) number of C's = 10,032,031 bp (19.27%) number of T's = 16,523,978 bp (31.74%) number of G's = 12,214,544 bp (23.46%) number of N's = 1,022 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 258,790 number of insertions = 4,324 mapped reads with insertion percentage = 0.48% number of deletions = 9,743 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.58% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.1844X There is a 1.57% of reference with a coverageData >= 1X There is a 0.07% 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 4423388 0.017746748161562253 0.2862181491161412 chr2 243199373 4151126 0.017068818676600782 0.2527315607171914 chr3 198022430 3040245 0.015353033492216008 0.13100405077216853 chr4 191154276 3237726 0.01693776392425561 0.14852305267051613 chr5 180915260 3010434 0.016640022516619106 0.13570873799457173 chr6 171115067 2793185 0.016323431062911602 0.15077294444509406 chr7 159138663 2997543 0.018836044889983774 0.23404263462330296 chr8 146364022 2805438 0.019167538317579166 0.23077100760110328 chr9 141213431 1730101 0.012251674559199684 0.13610208625282916 chr10 135534747 2286521 0.016870367567071196 0.19017201890152557 chr11 135006516 1863590 0.013803704111585251 0.14248479879998854 chr12 133851895 2597244 0.01940386424861598 0.147651097103915 chr13 115169878 1594418 0.013844053911388184 0.12334810503145749 chr14 107349540 1756600 0.016363367742423487 0.13600528094111738 chr15 102531392 1875572 0.018292661041800738 0.1421628784857054 chr16 90354753 1730857 0.01915623630779003 0.14976277364704083 chr17 81195210 2229037 0.0274528140268373 0.1781220440236671 chr18 78077248 970249 0.012426782767753289 0.2050027079745922 chr19 59128983 1241156 0.020990653602142962 0.22225063506751913 chr20 63025520 1504298 0.023868077566039914 0.16519962660972715 chr21 48129895 670525 0.013931569973298301 0.13531128671769668 chr22 51304566 454780 0.008864318236314483 0.09862281299045768 chrMT 16571 76343 4.607024319594473 3.3835338275977227 chrX 155270560 2849359 0.018350928856056162 0.14987224704331056 chrY 59373566 180699 0.003043425082468518 0.12971416944287817