BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,146,776 number of mapped reads = 3,077,646 (97.8%) number of supplementary alignments = 44,481 (1.41%) number of secondary alignments = 0 number of mapped bases = 284,997,523 bp number of sequenced bases = 284,831,576 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,601,788 duplication rate = 43.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1612 >>>>>>> ACTG content number of A's = 81,703,843 bp (28.68%) number of C's = 62,577,017 bp (21.97%) number of T's = 82,033,668 bp (28.8%) number of G's = 58,502,013 bp (20.54%) number of N's = 15,035 bp (0.01%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,791,878 number of insertions = 39,666 mapped reads with insertion percentage = 1.26% number of deletions = 89,389 mapped reads with deletion percentage = 2.85% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.0921X std coverageData = 1.0172X There is a 3.54% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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% 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 28253174 0.11335247184800394 1.887008940298614 chr2 243199373 22681624 0.09326349702390063 1.225362510985882 chr3 198022430 15737746 0.07947456255334308 0.5894348306972644 chr4 191154276 16034916 0.08388468380377742 0.6912648561851146 chr5 180915260 15223382 0.08414647830149873 0.6154452255704572 chr6 171115067 11980395 0.07001367682017154 0.707987865621861 chr7 159138663 14012856 0.08805437808661243 1.3370284966302957 chr8 146364022 26405817 0.18041193893947516 1.0033107739678357 chr9 141213431 12411368 0.08789084658668198 1.0233530743636492 chr10 135534747 14992802 0.110619618451053 1.1859420885254965 chr11 135006516 9570318 0.07088782292552458 0.6778286114893722 chr12 133851895 13317644 0.09949537135802224 0.673435101832103 chr13 115169878 6249392 0.05426238273865324 0.4814627249131543 chr14 107349540 6877087 0.06406256608086071 0.5467111445266871 chr15 102531392 7496163 0.07311090636514522 0.5700153689054375 chr16 90354753 8849212 0.09793853346043678 0.9753937009616654 chr17 81195210 10047093 0.12373997185301941 0.8398476851842227 chr18 78077248 6686838 0.08564387412835042 1.2191983889852487 chr19 59128983 5866766 0.09921980224148283 1.6725584881071878 chr20 63025520 8118840 0.12881829455750624 0.8209120404003033 chr21 48129895 3984804 0.08279270087748997 0.6485730004836368 chr22 51304566 2322377 0.04526647784136796 0.47681377642314604 chrMT 16571 62420 3.7668215557298894 4.744469179690815 chrX 155270560 16805281 0.10823224312451761 0.8032085307822218 chrY 59373566 1009208 0.01699759788724834 0.9049051749869551