BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084796.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 = 2,150,178 number of mapped reads = 1,939,712 (90.21%) number of supplementary alignments = 20,037 (0.93%) number of secondary alignments = 0 number of mapped bases = 128,982,174 bp number of sequenced bases = 128,934,399 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,223 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4067 >>>>>>> ACTG content number of A's = 34,947,528 bp (27.1%) number of C's = 24,236,844 bp (18.8%) number of T's = 40,419,227 bp (31.35%) number of G's = 29,313,171 bp (22.73%) number of N's = 17,629 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 980,322 number of insertions = 9,923 mapped reads with insertion percentage = 0.51% number of deletions = 29,401 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.294X There is a 3.46% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10763603 0.04318385630020156 0.37214737004286697 chr2 243199373 11999580 0.04934050549546441 0.48416542717683875 chr3 198022430 10686003 0.053963598972096245 0.27342013436015944 chr4 191154276 6253886 0.032716432668239134 0.2133864689232989 chr5 180915260 7598021 0.041997678913321075 0.24010353824152192 chr6 171115067 8299591 0.04850298191450318 0.27644827138027556 chr7 159138663 6698188 0.04209026187432528 0.29862143499164884 chr8 146364022 6277159 0.04288730874039523 0.28952740768909035 chr9 141213431 8521293 0.060343360682171936 0.3378256960351966 chr10 135534747 4080654 0.03010780696702079 0.2141060079778039 chr11 135006516 6102908 0.045204544053266286 0.299763037804513 chr12 133851895 4671714 0.03490211326481407 0.2197819880497175 chr13 115169878 3845552 0.033390258518811666 0.21388316726935908 chr14 107349540 2434737 0.022680460484506965 0.17971919921686708 chr15 102531392 3137322 0.03059864826569408 0.21289536648266097 chr16 90354753 2497620 0.027642375382288965 0.2015039659419177 chr17 81195210 3881152 0.047800258167938724 0.26279634741613717 chr18 78077248 5468406 0.07003840606677121 0.4274833828292383 chr19 59128983 3195919 0.054049957192735754 0.32220039006103873 chr20 63025520 2658282 0.04217786699736868 0.24405596835163237 chr21 48129895 1335352 0.02774475198834321 0.197917876836052 chr22 51304566 950501 0.018526635621476654 0.15587864629322615 chrMT 16571 7430 0.44837366483615954 0.7680239718462418 chrX 155270560 7382937 0.04754885278960802 0.26551169965460497 chrY 59373566 234364 0.003947278490902837 0.07997452676663527