BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230384.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 = 2,484,811 number of mapped reads = 2,124,706 (85.51%) number of supplementary alignments = 33,386 (1.34%) number of secondary alignments = 0 number of mapped bases = 138,874,021 bp number of sequenced bases = 138,815,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 292,905 duplication rate = 10.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6111 >>>>>>> ACTG content number of A's = 38,420,893 bp (27.68%) number of C's = 25,646,816 bp (18.48%) number of T's = 43,754,970 bp (31.52%) number of G's = 30,966,428 bp (22.31%) number of N's = 26,511 bp (0.02%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,208,710 number of insertions = 12,078 mapped reads with insertion percentage = 0.56% number of deletions = 35,363 mapped reads with deletion percentage = 1.65% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.4921X There is a 2.46% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% 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% 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 16301881 0.06540357225428939 0.807373242156144 chr2 243199373 6194540 0.02547103606225169 0.45851935014909484 chr3 198022430 12623936 0.06375003074146701 0.4117419235907289 chr4 191154276 10301886 0.05389304500831569 0.39632018334267327 chr5 180915260 4534529 0.0250643809704057 0.2557351534769114 chr6 171115067 9798536 0.05726284757846602 0.44089341667516085 chr7 159138663 11511421 0.07233579058031925 0.7187557548205096 chr8 146364022 4024278 0.027494994637411646 0.8470735449167436 chr9 141213431 4906216 0.03474326744458181 0.36213983077767053 chr10 135534747 7318183 0.05399488442620548 0.4649756082357982 chr11 135006516 5862556 0.04342424479719186 0.39826373138757976 chr12 133851895 8186067 0.06115764741320995 0.4031289967449412 chr13 115169878 6545858 0.05683654540295684 0.3880910489211449 chr14 107349540 3797493 0.03537502815568656 0.32179982910295013 chr15 102531392 3939215 0.03841959933597702 0.3177527628034644 chr16 90354753 2638211 0.029198364362746917 0.3081015963054794 chr17 81195210 2250521 0.027717410916235082 0.2822425929434647 chr18 78077248 3000182 0.03842581644271069 0.7286172833036713 chr19 59128983 2600001 0.043971684748915774 0.5062072781848083 chr20 63025520 1198061 0.019009141059050366 0.26928132764226964 chr21 48129895 1934565 0.04019466487512595 0.3400484580838003 chr22 51304566 1034970 0.02017305828101148 0.2236720229614243 chrMT 16571 9825 0.5929032647396053 1.1114098230085274 chrX 155270560 7961739 0.05127655236124607 0.38955527220886343 chrY 59373566 399351 0.006726074024255171 0.16265099095186533