BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240242.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 = 2,161,330 number of mapped reads = 1,860,827 (86.1%) number of supplementary alignments = 21,880 (1.01%) number of secondary alignments = 0 number of mapped bases = 121,955,155 bp number of sequenced bases = 121,893,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 273,138 duplication rate = 10.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8306 >>>>>>> ACTG content number of A's = 35,255,405 bp (28.92%) number of C's = 22,449,785 bp (18.42%) number of T's = 38,915,018 bp (31.93%) number of G's = 25,262,239 bp (20.72%) number of N's = 11,255 bp (0.01%) GC percentage = 39.14% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,059,430 number of insertions = 9,942 mapped reads with insertion percentage = 0.53% number of deletions = 35,115 mapped reads with deletion percentage = 1.86% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.0394X std coverageData = 0.7059X There is a 1.78% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.16% 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 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 16491316 0.06616359042090411 1.4797441621825325 chr2 243199373 2997948 0.012327120596647262 0.48124370763716384 chr3 198022430 1878124 0.00948440032778105 0.17074946197832452 chr4 191154276 13067172 0.06835929738762422 0.5165849797557548 chr5 180915260 1871509 0.010344671864606667 0.18884906419160588 chr6 171115067 4876487 0.02849829115281824 0.3147309939683835 chr7 159138663 10794635 0.0678316305824437 0.6026650433416929 chr8 146364022 5393689 0.036851194209462215 1.4559198896143317 chr9 141213431 8425616 0.059665825979399935 0.6901234421128386 chr10 135534747 3691090 0.027233532962584125 0.41423705792653454 chr11 135006516 8685647 0.06433502068892734 0.6672261233646164 chr12 133851895 1908121 0.01425546496745526 0.23639578413794 chr13 115169878 8011126 0.0695592123489095 0.5029626627511841 chr14 107349540 7225956 0.06731240767310227 0.5375510915528495 chr15 102531392 2013577 0.019638639061878727 0.2604288192727819 chr16 90354753 5461420 0.06044419157451518 0.5219480888725149 chr17 81195210 2420789 0.029814431171493985 0.3418419142745103 chr18 78077248 5427011 0.06950822600714615 1.4080153582627413 chr19 59128983 4436508 0.07503102158885432 0.8817513186608663 chr20 63025520 2789629 0.044261895816170974 0.3947678525936426 chr21 48129895 608195 0.012636532865903822 0.26490601758196786 chr22 51304566 1011988 0.01972510594865962 0.24418846827673937 chrMT 16571 44891 2.709009715768511 3.4095785947536545 chrX 155270560 2118779 0.013645722666292954 0.2734621965788884 chrY 59373566 303932 0.005118978368252296 0.18783915413330596