BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514707.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 75,538,672 number of mapped reads = 74,848,939 (99.09%) number of supplementary alignments = 3,870,296 (5.12%) number of secondary alignments = 0 number of mapped bases = 7,119,205,699 bp number of sequenced bases = 7,112,846,990 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,555,154 duplication rate = 33.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2193 >>>>>>> ACTG content number of A's = 2,108,139,717 bp (29.64%) number of C's = 1,440,419,588 bp (20.25%) number of T's = 2,086,999,489 bp (29.34%) number of G's = 1,467,126,529 bp (20.63%) number of N's = 10,161,667 bp (0.14%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 44,515,535 number of insertions = 2,599,908 mapped reads with insertion percentage = 3.31% number of deletions = 2,658,596 mapped reads with deletion percentage = 3.34% homopolymer indels = 39.79% >>>>>>> Coverage mean coverageData = 2.2997X std coverageData = 150.1757X There is a 13.52% of reference with a coverageData >= 1X There is a 10.09% of reference with a coverageData >= 2X There is a 8.42% of reference with a coverageData >= 3X There is a 7.38% of reference with a coverageData >= 4X There is a 6.62% of reference with a coverageData >= 5X There is a 6.02% of reference with a coverageData >= 6X There is a 5.54% of reference with a coverageData >= 7X There is a 5.14% of reference with a coverageData >= 8X There is a 4.79% of reference with a coverageData >= 9X There is a 4.49% of reference with a coverageData >= 10X There is a 4.22% of reference with a coverageData >= 11X There is a 3.99% of reference with a coverageData >= 12X There is a 3.77% of reference with a coverageData >= 13X There is a 3.58% of reference with a coverageData >= 14X There is a 3.41% of reference with a coverageData >= 15X There is a 3.24% of reference with a coverageData >= 16X There is a 3.1% of reference with a coverageData >= 17X There is a 2.96% of reference with a coverageData >= 18X There is a 2.83% of reference with a coverageData >= 19X There is a 2.71% of reference with a coverageData >= 20X There is a 2.6% of reference with a coverageData >= 21X There is a 2.5% of reference with a coverageData >= 22X There is a 2.4% of reference with a coverageData >= 23X There is a 2.31% of reference with a coverageData >= 24X There is a 2.22% of reference with a coverageData >= 25X There is a 2.14% of reference with a coverageData >= 26X There is a 2.07% of reference with a coverageData >= 27X There is a 1.99% of reference with a coverageData >= 28X There is a 1.92% of reference with a coverageData >= 29X There is a 1.86% of reference with a coverageData >= 30X There is a 1.8% of reference with a coverageData >= 31X There is a 1.74% of reference with a coverageData >= 32X There is a 1.68% of reference with a coverageData >= 33X There is a 1.63% of reference with a coverageData >= 34X There is a 1.58% of reference with a coverageData >= 35X There is a 1.53% of reference with a coverageData >= 36X There is a 1.48% of reference with a coverageData >= 37X There is a 1.44% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.35% of reference with a coverageData >= 40X There is a 1.32% of reference with a coverageData >= 41X There is a 1.28% of reference with a coverageData >= 42X There is a 1.24% of reference with a coverageData >= 43X There is a 1.21% of reference with a coverageData >= 44X There is a 1.17% of reference with a coverageData >= 45X There is a 1.14% of reference with a coverageData >= 46X There is a 1.11% of reference with a coverageData >= 47X There is a 1.08% of reference with a coverageData >= 48X There is a 1.05% of reference with a coverageData >= 49X There is a 1.03% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 604415805 2.4249319924462696 22.832456655465315 chr2 243199373 606821285 2.495159742866607 121.9002042440278 chr3 198022430 461160869 2.328831481362995 28.0033921031561 chr4 191154276 486508677 2.545110092122658 14.706880368738066 chr5 180915260 443347778 2.4505825434515587 15.711646119571135 chr6 171115067 303799163 1.7754086085242278 17.31500095298506 chr7 159138663 455424800 2.8618111489349385 57.97672041522748 chr8 146364022 538890082 3.681848002236506 621.0072188489612 chr9 141213431 309522861 2.191879758236311 184.49457025449453 chr10 135534747 389609094 2.87460671616556 17.82487703940723 chr11 135006516 349766295 2.5907363982342897 76.79630752594937 chr12 133851895 258695341 1.9326983827909199 14.41308313949033 chr13 115169878 245856290 2.1347273633475585 34.38944263642162 chr14 107349540 226216896 2.107292644197637 14.427745699599773 chr15 102531392 179262483 1.748366812380739 13.747660097725504 chr16 90354753 182473176 2.0195193937390323 34.69418873604748 chr17 81195210 99228127 1.2220933599408141 12.214302611996978 chr18 78077248 304132852 3.8952814013116854 20.910469388224435 chr19 59128983 138040421 2.334564438559682 25.813651331363474 chr20 63025520 188832230 2.996123316396279 18.227750524963298 chr21 48129895 114318613 2.3752101059019557 235.84986819381433 chr22 51304566 55582510 1.0833832996462731 27.63792062741864 chrMT 16571 1678681 101.302335405226 65.43821660043656 chrX 155270560 164633862 1.060303137954806 9.610463623188897 chrY 59373566 10987508 0.18505723574022823 2.426394276246047