BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524609.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 = 2,212,496 number of mapped reads = 2,057,388 (92.99%) number of supplementary alignments = 4,371 (0.2%) number of secondary alignments = 0 number of mapped bases = 120,037,698 bp number of sequenced bases = 119,999,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,912 duplication rate = 4.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6028 >>>>>>> ACTG content number of A's = 30,894,949 bp (25.75%) number of C's = 21,042,953 bp (17.54%) number of T's = 37,893,632 bp (31.58%) number of G's = 30,167,318 bp (25.14%) number of N's = 705 bp (0%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 549,978 number of insertions = 6,474 mapped reads with insertion percentage = 0.31% number of deletions = 22,417 mapped reads with deletion percentage = 1.08% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3366X There is a 3.31% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12339596 0.04950678136926287 0.6297992404318318 chr2 243199373 10959947 0.045065687731028814 0.38760200603167355 chr3 198022430 7712147 0.038945825480477134 0.2271959550040143 chr4 191154276 5418076 0.02834399582042308 0.2258058760062497 chr5 180915260 7133395 0.0394294820680135 0.22629326353273704 chr6 171115067 7767784 0.04539509077830066 0.268221046635926 chr7 159138663 7373894 0.04633628221446098 0.4441409428658543 chr8 146364022 10657787 0.07281698640394017 0.44465582265436304 chr9 141213431 4371289 0.03095519292353997 0.2956511636855547 chr10 135534747 5079158 0.03747495098065148 0.3265552023561059 chr11 135006516 6047890 0.04479702298220924 0.3249498487915213 chr12 133851895 3995782 0.02985226320479064 0.20660722862687095 chr13 115169878 2977886 0.02585646569843549 0.1879452594949616 chr14 107349540 2162727 0.020146588425064515 0.17035030025231934 chr15 102531392 3051336 0.029760017302798345 0.20917853933286806 chr16 90354753 3461665 0.03831193030874646 0.23958567791900148 chr17 81195210 2574846 0.031711796791953614 0.21070727864961422 chr18 78077248 3569811 0.04572152696775378 0.4725188691138702 chr19 59128983 2278561 0.038535433629900244 0.4212755174068416 chr20 63025520 2199208 0.03489392868158803 0.21907386975423856 chr21 48129895 1033733 0.021477981616207557 0.1897432340329486 chr22 51304566 2080826 0.04055830040546489 0.22961484128671777 chrMT 16571 2319 0.13994327439502746 0.43380697869052515 chrX 155270560 5492546 0.035374033557939125 0.24532221265066903 chrY 59373566 295489 0.004976777039128827 0.13981182554741708