BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525222.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 = 1,209,676 number of mapped reads = 1,096,885 (90.68%) number of supplementary alignments = 3,121 (0.26%) number of secondary alignments = 0 number of mapped bases = 63,510,703 bp number of sequenced bases = 63,490,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,566 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8076 >>>>>>> ACTG content number of A's = 15,064,487 bp (23.73%) number of C's = 11,135,741 bp (17.54%) number of T's = 21,025,893 bp (33.12%) number of G's = 16,262,953 bp (25.61%) number of N's = 1,387 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 329,206 number of insertions = 4,320 mapped reads with insertion percentage = 0.39% number of deletions = 12,783 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2087X There is a 1.9% of reference with a coverageData >= 1X There is a 0.11% 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 6898919 0.027678643175777683 0.3604977248701473 chr2 243199373 5445957 0.02239297302793622 0.2698259887334859 chr3 198022430 5179849 0.02615789029555894 0.17479314169127438 chr4 191154276 3740404 0.019567461833812184 0.15692378892880346 chr5 180915260 2944080 0.016273254119083154 0.1351405840833917 chr6 171115067 3250659 0.01899691860565382 0.16159839934250833 chr7 159138663 3784975 0.02378413220676612 0.2870783954809019 chr8 146364022 2974009 0.02031926261222857 0.18922670370114308 chr9 141213431 2124892 0.015047378885652881 0.15142588001437246 chr10 135534747 3554820 0.026228108132300566 0.2525744081383659 chr11 135006516 2972148 0.022014848527755506 0.18141696281940434 chr12 133851895 2951638 0.022051521945206678 0.15914089188000824 chr13 115169878 2010292 0.017455015451175525 0.14223134019053763 chr14 107349540 1859174 0.017318881850821158 0.14250655444588028 chr15 102531392 1833306 0.01788043607171548 0.1442335544963482 chr16 90354753 1756736 0.01944265178833481 0.16261841171115773 chr17 81195210 1632388 0.020104486459238173 0.1537126936657734 chr18 78077248 1402118 0.017958086842405102 0.253370782873071 chr19 59128983 1173370 0.01984424457291951 0.2674024159025809 chr20 63025520 1204291 0.019107989906310966 0.14910714401932365 chr21 48129895 828022 0.017203902065441864 0.14603415460173422 chr22 51304566 532353 0.0103763279081242 0.1085878278364971 chrMT 16571 4290 0.2588860056725605 0.5774397532364297 chrX 155270560 3261784 0.021007098834447433 0.16577896276355147 chrY 59373566 190229 0.003203934222175572 0.09291224019719341