BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975255.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,522,864 number of mapped reads = 5,481,136 (99.24%) number of supplementary alignments = 13,941 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,740,174 number of mapped paired reads (second in pair) = 2,740,962 number of mapped paired reads (both in pair) = 5,469,844 number of mapped paired reads (singletons) = 11,292 number of mapped bases = 506,160,496 bp number of sequenced bases = 505,925,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,064 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 69,799.5546 std insert size = 2,565,101.2237 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 52.9131 >>>>>>> ACTG content number of A's = 146,475,752 bp (28.95%) number of C's = 101,908,849 bp (20.14%) number of T's = 149,104,508 bp (29.47%) number of G's = 108,429,676 bp (21.43%) number of N's = 7,165 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 3,289,009 number of insertions = 78,246 mapped reads with insertion percentage = 1.41% number of deletions = 146,766 mapped reads with deletion percentage = 2.63% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.1635X std coverageData = 1.1199X There is a 10.21% of reference with a coverageData >= 1X There is a 3.66% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% 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 36815922 0.14770644041845737 1.1685625624325204 chr2 243199373 44486607 0.18292237537964376 1.3541139385580894 chr3 198022430 29532990 0.1491396201935306 0.5519940517708183 chr4 191154276 21061345 0.11017982668616841 0.5632838055120961 chr5 180915260 32414207 0.17916789882732945 0.5829725745616189 chr6 171115067 50334312 0.2941547631220575 1.9602786344559369 chr7 159138663 23921037 0.15031568412762145 1.0957564464386422 chr8 146364022 48074104 0.3284557457706375 0.9300388641643406 chr9 141213431 14899815 0.10551273270883135 1.007800321233758 chr10 135534747 19573945 0.14442012423574302 1.248913739631074 chr11 135006516 31072467 0.23015531339242914 1.5057228988152709 chr12 133851895 26108124 0.19505233003985487 0.6143751716513923 chr13 115169878 15854194 0.13765920634213052 0.5222304631338535 chr14 107349540 9694747 0.09031009355047073 0.4177509589537187 chr15 102531392 5565543 0.05428135609433645 0.3103300403902236 chr16 90354753 23044041 0.2550396103678132 2.581439662238828 chr17 81195210 15815145 0.19477928562534663 1.965162101812607 chr18 78077248 9963082 0.12760544531487586 0.9498600962615376 chr19 59128983 6291408 0.1064014241543779 0.6892722276978884 chr20 63025520 13063934 0.20728006686815117 0.6472713722168641 chr21 48129895 5422768 0.11266943341555181 0.48365311401240696 chr22 51304566 4363085 0.08504282055519191 0.39323859443667764 chrMT 16571 114956 6.937179409812323 5.369976490212507 chrX 155270560 18200789 0.11721983227213195 0.7528583576074626 chrY 59373566 471929 0.007948469862834245 0.2452281594289146