BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006403.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,620,112 number of mapped reads = 4,965,056 (88.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,498,029 number of mapped paired reads (second in pair) = 2,467,027 number of mapped paired reads (both in pair) = 4,584,612 number of mapped paired reads (singletons) = 380,444 number of mapped bases = 192,242,677 bp number of sequenced bases = 192,219,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,307 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 74,086.8395 std insert size = 2,586,465.8579 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 48.0715 >>>>>>> ACTG content number of A's = 52,511,946 bp (27.32%) number of C's = 42,302,690 bp (22.01%) number of T's = 53,574,468 bp (27.87%) number of G's = 43,821,583 bp (22.8%) number of N's = 8,363 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 578,534 number of insertions = 5,337 mapped reads with insertion percentage = 0.11% number of deletions = 17,801 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.07% >>>>>>> Coverage mean coverageData = 0.0621X std coverageData = 0.3631X There is a 5.23% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.13% 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 0.01% 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 16225997 0.06509912366477114 0.4333606318781276 chr2 243199373 15195811 0.06248293658224193 0.33881383613590266 chr3 198022430 12694953 0.0641086618318945 0.2890712670325904 chr4 191154276 11646528 0.060927373657076865 0.3130703854507362 chr5 180915260 11210770 0.061966967297286034 0.28452380746191186 chr6 171115067 11128988 0.06503803665635124 0.3156935938158643 chr7 159138663 10648141 0.06691108747093093 0.39638916083602166 chr8 146364022 9384953 0.06412062795049456 0.5931693904068889 chr9 141213431 8192211 0.05801297328438964 0.309959436143159 chr10 135534747 9582060 0.07069818044519609 0.37457532950975236 chr11 135006516 8757838 0.0648697430278106 0.33139281151886857 chr12 133851895 8602547 0.06426914613349329 0.2904164117104426 chr13 115169878 5713167 0.049606434418555174 0.25248076017389326 chr14 107349540 5828692 0.054296385433975775 0.6190904938425905 chr15 102531392 5568986 0.05431493605392581 0.2660876940015694 chr16 90354753 6119922 0.06773215350386715 0.3294088545461748 chr17 81195210 5763517 0.07098346072385305 0.31574966536755794 chr18 78077248 4940400 0.06327579578624493 0.4553646081646674 chr19 59128983 4503185 0.07615867501052741 0.38807490219512103 chr20 63025520 4368851 0.06931876166987595 0.3149374197511947 chr21 48129895 2361655 0.04906835969619298 0.2960952160039945 chr22 51304566 2855315 0.055654208243375455 0.2819029956688863 chrMT 16571 8791 0.5305050992698087 0.8120520678445262 chrX 155270560 10477773 0.06748074457901099 0.3133040220333833 chrY 59373566 461626 0.007774941461323041 0.2003357863055363