BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240255.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,362,508 number of mapped reads = 1,848,012 (78.22%) number of supplementary alignments = 7,348 (0.31%) number of secondary alignments = 0 number of mapped bases = 112,513,107 bp number of sequenced bases = 112,449,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,901 duplication rate = 7.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2403 >>>>>>> ACTG content number of A's = 30,286,613 bp (26.93%) number of C's = 19,413,639 bp (17.26%) number of T's = 36,663,144 bp (32.6%) number of G's = 26,060,673 bp (23.18%) number of N's = 25,739 bp (0.02%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,069,619 number of insertions = 7,712 mapped reads with insertion percentage = 0.41% number of deletions = 36,790 mapped reads with deletion percentage = 1.97% homopolymer indels = 49.64% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3326X There is a 2.72% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 8340679 0.03346302194368454 0.4709755299689546 chr2 243199373 12278237 0.05048630203499743 0.4120627718165934 chr3 198022430 7709033 0.03893009998917799 0.2554078107709984 chr4 191154276 7386976 0.038644053141662395 0.25949140381640756 chr5 180915260 5999363 0.033161177227393646 0.23602162576593097 chr6 171115067 6306224 0.036853703829599065 0.28658809934139406 chr7 159138663 6943034 0.04362883204567328 0.5827896369088481 chr8 146364022 6512584 0.044495798291194814 0.43419546200340725 chr9 141213431 4042626 0.02862777266561847 0.28661898183161433 chr10 135534747 4926417 0.03634800011837555 0.276471767878038 chr11 135006516 5096443 0.037749607581903676 0.31566678544739096 chr12 133851895 5132222 0.03834254270363524 0.2543825294223297 chr13 115169878 2665189 0.023141372086892372 0.19622553479792626 chr14 107349540 3879301 0.03613709942306227 0.25282156308171666 chr15 102531392 2914763 0.028428005737013696 0.22798271217974503 chr16 90354753 3342387 0.03699182266593103 0.2526887296093304 chr17 81195210 2956978 0.036418133532753964 0.26333615097638235 chr18 78077248 2605248 0.03336756951269594 0.42565539967779975 chr19 59128983 1995719 0.033751958832101005 0.3349289076581396 chr20 63025520 2337944 0.037095195723890896 0.25072359627037155 chr21 48129895 1801680 0.037433698951555995 0.25546412320927425 chr22 51304566 1044192 0.02035280836407426 0.17916094334739438 chrMT 16571 54689 3.3002836280248626 4.13954144513142 chrX 155270560 6012249 0.038721113648331015 0.2742766133826234 chrY 59373566 228930 0.003855756280496947 0.08096658319234783