BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328243.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 41,713,784 number of mapped reads = 39,231,856 (94.05%) number of supplementary alignments = 445,260 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,659,581 number of mapped paired reads (second in pair) = 19,572,275 number of mapped paired reads (both in pair) = 38,330,562 number of mapped paired reads (singletons) = 901,294 number of mapped bases = 2,642,268,403 bp number of sequenced bases = 2,640,883,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,117,439 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 166,725.5052 std insert size = 3,909,777.0882 median insert size = 348 >>>>>>> Mapping quality mean mapping quality = 51.7131 >>>>>>> ACTG content number of A's = 776,639,630 bp (29.41%) number of C's = 537,805,522 bp (20.36%) number of T's = 768,916,598 bp (29.12%) number of G's = 557,433,224 bp (21.11%) number of N's = 88,999 bp (0%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 24,320,400 number of insertions = 260,343 mapped reads with insertion percentage = 0.66% number of deletions = 1,027,197 mapped reads with deletion percentage = 2.58% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.8535X std coverageData = 9.4878X There is a 49.48% of reference with a coverageData >= 1X There is a 19.99% of reference with a coverageData >= 2X There is a 7.03% of reference with a coverageData >= 3X There is a 2.43% of reference with a coverageData >= 4X There is a 0.95% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 210571198 0.8448171449089389 21.72440837107744 chr2 243199373 221324941 0.9100555575856686 14.181925451575585 chr3 198022430 195824163 0.9888988989782622 1.5666002366354241 chr4 191154276 156121786 0.8167318527575078 3.015796992737639 chr5 180915260 182507616 1.0088016676979046 1.1865569345278997 chr6 171115067 128596135 0.7515184796672522 3.7660058781599024 chr7 159138663 182997471 1.1499246477897078 5.942958629507527 chr8 146364022 152115475 1.0392955380797064 12.693219145507452 chr9 141213431 85650429 0.6065317469695924 3.9358020230750195 chr10 135534747 132127456 0.9748603876465716 16.705944879534236 chr11 135006516 92334964 0.683929685290153 2.7557648115862645 chr12 133851895 131478596 0.9822692162856567 1.257823117974807 chr13 115169878 69474939 0.6032387999924772 0.9383176442117264 chr14 107349540 98988844 0.9221170766078737 1.4297335393347441 chr15 102531392 82569608 0.8053105140716318 1.2595274814867545 chr16 90354753 86156865 0.9535399316514096 7.633120423194287 chr17 81195210 89552946 1.1029338553345696 3.254323559900698 chr18 78077248 64919466 0.8314773850635719 7.581911340381444 chr19 59128983 46385521 0.7844802776330518 12.432747078227434 chr20 63025520 88185195 1.399198213675984 2.8369946306986655 chr21 48129895 29784990 0.6188459376443685 1.8152989959819186 chr22 51304566 23333835 0.4548101040363542 0.9201626233412228 chrMT 16571 15065012 909.119063424054 194.83993771980892 chrX 155270560 69980738 0.4507019102655391 1.3988474302065335 chrY 59373566 6220214 0.10476402916408963 4.261093836286086