BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867851.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 = 2,052,657 number of mapped reads = 1,894,631 (92.3%) number of supplementary alignments = 8,373 (0.41%) number of secondary alignments = 0 number of mapped bases = 112,035,768 bp number of sequenced bases = 112,002,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,073 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9313 >>>>>>> ACTG content number of A's = 27,195,522 bp (24.28%) number of C's = 22,901,848 bp (20.45%) number of T's = 35,800,396 bp (31.96%) number of G's = 26,090,348 bp (23.29%) number of N's = 14,346 bp (0.01%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 564,394 number of insertions = 7,038 mapped reads with insertion percentage = 0.37% number of deletions = 20,898 mapped reads with deletion percentage = 1.09% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3485X There is a 3.18% of reference with a coverageData >= 1X There is a 0.31% 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 9053481 0.03632280218070149 0.6667527427374358 chr2 243199373 9401322 0.03865685130693162 0.46970707734937256 chr3 198022430 7399435 0.037366650838493394 0.21396898759495594 chr4 191154276 7165962 0.037487845681254864 0.2492445741035424 chr5 180915260 6788907 0.0375253419750219 0.21745010738884316 chr6 171115067 6389321 0.03733932442080042 0.24717502235031943 chr7 159138663 6173424 0.0387927351130253 0.4042398235328375 chr8 146364022 5734720 0.03918121353620632 0.3844542634343613 chr9 141213431 4737790 0.03355056219829401 0.2777736507771644 chr10 135534747 5453904 0.04023989508756747 0.35501444133259447 chr11 135006516 5074291 0.03758552661265624 0.297164020678032 chr12 133851895 5051884 0.03774234201166894 0.21890247834844456 chr13 115169878 3527525 0.030628885445202956 0.19402394800066625 chr14 107349540 3321676 0.03094261978206893 0.20270199511205528 chr15 102531392 3247710 0.03167527463198783 0.19634712600066168 chr16 90354753 3298519 0.03650631417253722 0.23268307910276217 chr17 81195210 3098406 0.03815996042131057 0.2323325059190506 chr18 78077248 3008056 0.038526665284104276 0.5178626496485843 chr19 59128983 2332535 0.03944825162983101 0.48896448492113814 chr20 63025520 2404663 0.03815379865172076 0.2236059250909064 chr21 48129895 1485049 0.030855022642372273 0.23671491118172083 chr22 51304566 1353181 0.02637544970168932 0.18038803905776218 chrMT 16571 37225 2.2463943033009475 2.007039412703172 chrX 155270560 6121626 0.03942554209890143 0.24366716591548668 chrY 59373566 375156 0.0063185694455340615 0.24370438706357697