BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004150.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 = 3,991,548 number of mapped reads = 3,247,131 (81.35%) number of supplementary alignments = 22,884 (0.57%) number of secondary alignments = 0 number of mapped bases = 208,172,655 bp number of sequenced bases = 208,067,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,683 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.28 >>>>>>> ACTG content number of A's = 55,098,006 bp (26.48%) number of C's = 38,382,392 bp (18.45%) number of T's = 65,165,526 bp (31.32%) number of G's = 49,400,462 bp (23.74%) number of N's = 20,651 bp (0.01%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,152,732 number of insertions = 21,293 mapped reads with insertion percentage = 0.65% number of deletions = 62,325 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0672X std coverageData = 0.7301X There is a 5.28% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 20587017 0.0825956497817512 1.2093521566966798 chr2 243199373 19358205 0.07959808761513543 1.1358823936918854 chr3 198022430 14119622 0.07130314480031379 0.3327945066726134 chr4 191154276 11250062 0.05885331071537212 0.3294025250401615 chr5 180915260 11416987 0.06310682139251271 0.3235193029824821 chr6 171115067 12833637 0.07500004076204464 0.49306719059458726 chr7 159138663 10939146 0.0687397128628635 0.9383799262851283 chr8 146364022 11705268 0.07997367003210666 0.7535859002472778 chr9 141213431 7960770 0.05637402861488437 0.8229141220445966 chr10 135534747 9286365 0.06851648898566211 0.5426156454194162 chr11 135006516 8948355 0.06628091195242754 0.6753869612790555 chr12 133851895 8680605 0.06485231307334124 0.3426431804007757 chr13 115169878 4725529 0.041030945608885684 0.24386749905270777 chr14 107349540 5189031 0.04833771062270038 0.4251094422003328 chr15 102531392 5401252 0.05267900781060302 0.31142793969578886 chr16 90354753 7195286 0.07963372994888271 0.47311037384687216 chr17 81195210 5847811 0.07202162541361738 0.4263022191596293 chr18 78077248 6275450 0.08037488718864681 1.7758765273349177 chr19 59128983 5043805 0.08530173772817977 0.9213714743471612 chr20 63025520 4411793 0.07000010471948506 0.39639685979918465 chr21 48129895 3670941 0.07627153560172945 0.4069438657236166 chr22 51304566 3045152 0.05935440521999543 0.3041452662578903 chrMT 16571 111127 6.706113089131615 6.335001341137534 chrX 155270560 9626332 0.061997148718984464 0.49494174667558666 chrY 59373566 543107 0.009147286184562335 0.18762025558893938