BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084855.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,494,702 number of mapped reads = 2,252,855 (90.31%) number of supplementary alignments = 20,772 (0.83%) number of secondary alignments = 0 number of mapped bases = 157,063,271 bp number of sequenced bases = 157,003,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,892 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4026 >>>>>>> ACTG content number of A's = 45,769,118 bp (29.15%) number of C's = 28,873,392 bp (18.39%) number of T's = 50,529,960 bp (32.18%) number of G's = 31,805,470 bp (20.26%) number of N's = 25,518 bp (0.02%) GC percentage = 38.65% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,265,987 number of insertions = 12,445 mapped reads with insertion percentage = 0.55% number of deletions = 34,025 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.6% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.4087X There is a 3.89% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12677246 0.05086144198613651 0.5992186776792793 chr2 243199373 13725179 0.05643591441331553 0.344861383176866 chr3 198022430 11023319 0.055667022165115335 0.29292600015737313 chr4 191154276 11505568 0.06018995881630187 0.3109468590906381 chr5 180915260 10652897 0.05888335234960279 0.3031460269572747 chr6 171115067 9430612 0.055112692092742485 0.2954557483256113 chr7 159138663 8877398 0.05578404287586606 0.3841526428029901 chr8 146364022 8038945 0.054924324230445104 1.0544596671290585 chr9 141213431 6606971 0.046787128909855605 0.31738461649046756 chr10 135534747 7070326 0.052166150426355244 0.3268419602831849 chr11 135006516 7125953 0.05278228941186809 0.31032173825935955 chr12 133851895 7215381 0.053905706751480806 0.2888683538637745 chr13 115169878 5265748 0.04572157313564229 0.26587944442466516 chr14 107349540 4602428 0.04287329037460244 0.2666264478393556 chr15 102531392 4448876 0.043390379406923495 0.25688597033291605 chr16 90354753 3823197 0.042313180801899816 0.2677586650116958 chr17 81195210 3535096 0.04353823335145016 0.2685613671421681 chr18 78077248 4197747 0.05376402354755127 0.5376873216702013 chr19 59128983 2299244 0.03888522824754148 0.4095849673611528 chr20 63025520 2798753 0.04440666257097125 0.2656250286584157 chr21 48129895 1855533 0.03855260851909193 0.2515668624193421 chr22 51304566 1264410 0.024645174856366584 0.18989734758450869 chrMT 16571 103651 6.254963490435097 3.8560398601378187 chrX 155270560 8595976 0.055361273895064206 0.2996033103763091 chrY 59373566 322817 0.005437049208060031 0.10872570222114081