BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124916.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,232,704 number of mapped reads = 2,214,777 (99.2%) number of supplementary alignments = 608,810 (27.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,108,579 number of mapped paired reads (second in pair) = 1,106,198 number of mapped paired reads (both in pair) = 2,207,548 number of mapped paired reads (singletons) = 7,229 number of mapped bases = 298,793,981 bp number of sequenced bases = 298,413,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 799,433 duplication rate = 24.81% >>>>>>> Insert size mean insert size = 1,189,901.8424 std insert size = 10,335,033.7082 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 47.0967 >>>>>>> ACTG content number of A's = 86,232,842 bp (28.9%) number of C's = 62,516,035 bp (20.95%) number of T's = 86,085,172 bp (28.85%) number of G's = 63,560,826 bp (21.3%) number of N's = 18,219 bp (0.01%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0182 number of mismatches = 5,110,085 number of insertions = 106,201 mapped reads with insertion percentage = 4.47% number of deletions = 182,669 mapped reads with deletion percentage = 7.82% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.0965X std coverageData = 5.0868X There is a 4.31% of reference with a coverageData >= 1X There is a 2.58% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 24617198 0.09876484119170961 2.6012321291594795 chr2 243199373 25046376 0.10298700893443503 3.0664565962563297 chr3 198022430 16201854 0.0818182768487388 1.615261353937291 chr4 191154276 18149330 0.09494597965467433 2.40843259015142 chr5 180915260 14590508 0.0806482990987051 0.46679810742444056 chr6 171115067 14289062 0.08350557464352336 1.2428370116809537 chr7 159138663 13696390 0.08606576014780268 2.2886549604101067 chr8 146364022 15420182 0.10535500315781156 0.9372704515894951 chr9 141213431 10174066 0.0720474386037685 3.1079754271586286 chr10 135534747 28807487 0.21254687552558016 21.977144631498142 chr11 135006516 10084257 0.07469459474089384 1.111687119962494 chr12 133851895 15388625 0.11496755425091292 0.5732146899855903 chr13 115169878 6861061 0.0595733981762141 0.3743996915271144 chr14 107349540 7112958 0.06625979021428503 0.4643379001982452 chr15 102531392 6725177 0.06559139468232325 0.3913928192394825 chr16 90354753 15638855 0.1730828150235771 5.65201074231573 chr17 81195210 7446425 0.09171015137469317 3.0822995701660005 chr18 78077248 7025332 0.0899792472193692 2.5914327502955263 chr19 59128983 4394744 0.07432470130595685 1.4771354533278 chr20 63025520 8019338 0.12723953725411546 0.9506132589222807 chr21 48129895 3201344 0.06651466827426072 1.5069898195010552 chr22 51304566 1646179 0.032086403381718503 0.34407282303885883 chrMT 16571 34561 2.0856315249532313 2.5363680444926016 chrX 155270560 21250708 0.13686244192073502 1.2601047906492495 chrY 59373566 2971964 0.050055339441798054 4.876972378246367