BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751185.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,282,207 number of mapped reads = 4,884,518 (92.47%) number of supplementary alignments = 171,493 (3.25%) number of secondary alignments = 0 number of mapped bases = 479,434,265 bp number of sequenced bases = 479,289,718 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,591 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2647 >>>>>>> ACTG content number of A's = 138,261,381 bp (28.85%) number of C's = 101,530,777 bp (21.18%) number of T's = 139,154,847 bp (29.03%) number of G's = 100,340,215 bp (20.94%) number of N's = 2,498 bp (0%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,698,942 number of insertions = 150,644 mapped reads with insertion percentage = 3.01% number of deletions = 66,669 mapped reads with deletion percentage = 1.34% homopolymer indels = 49.97% >>>>>>> Coverage mean coverageData = 0.1549X std coverageData = 1.225X There is a 12.05% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 59068502 0.23698437244816334 3.432127227910244 chr2 243199373 35656651 0.14661489690600477 0.5403451006324981 chr3 198022430 31290610 0.1580154833975121 0.4923063634634527 chr4 191154276 20079353 0.10504265674914852 0.43174578690939924 chr5 180915260 37497261 0.20726422414560275 0.5422235695407339 chr6 171115067 26159025 0.15287388456564144 0.8089961645250072 chr7 159138663 25555184 0.16058438294156085 0.686686277441668 chr8 146364022 22690744 0.15502951948122878 0.552679013882869 chr9 141213431 20765219 0.14704847019827738 0.6106875633876203 chr10 135534747 23888169 0.17625125311961515 1.5663884380135433 chr11 135006516 22093108 0.16364475326509426 0.6541517207308494 chr12 133851895 25760954 0.19245864244208122 0.5190396255053068 chr13 115169878 12555111 0.10901384301197228 0.3860982902137832 chr14 107349540 10453923 0.09738209404530285 0.3783274028712456 chr15 102531392 12457670 0.1215010325813191 0.4106760232604698 chr16 90354753 14565881 0.16120768987105746 0.845112367566888 chr17 81195210 15450485 0.19028813399214067 0.7010158964456809 chr18 78077248 9511187 0.1218176516672309 1.1484418073407996 chr19 59128983 10582913 0.1789801289157975 2.4195540555485566 chr20 63025520 9251369 0.14678766632944876 0.4576609022046976 chr21 48129895 5938002 0.12337450559574252 0.4439026481370694 chr22 51304566 6760846 0.13177864130065928 0.4377105111302321 chrMT 16571 1157966 69.87906583790961 27.5846715766783 chrX 155270560 19239661 0.12391055329484224 0.45697003967623245 chrY 59373566 1004471 0.016917814907731834 0.6341102866327121