BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472516.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,984,494 number of mapped reads = 15,793,244 (98.8%) number of supplementary alignments = 69,497 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,921,475 number of mapped paired reads (second in pair) = 7,871,769 number of mapped paired reads (both in pair) = 15,696,920 number of mapped paired reads (singletons) = 96,324 number of mapped bases = 1,550,765,450 bp number of sequenced bases = 1,550,579,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,091,138 duplication rate = 44.81% >>>>>>> Insert size mean insert size = 28,792.8277 std insert size = 1,674,134.4608 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 54.9329 >>>>>>> ACTG content number of A's = 428,929,418 bp (27.66%) number of C's = 348,865,962 bp (22.5%) number of T's = 425,323,138 bp (27.43%) number of G's = 347,221,094 bp (22.39%) number of N's = 239,889 bp (0.02%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,338,803 number of insertions = 78,938 mapped reads with insertion percentage = 0.49% number of deletions = 74,827 mapped reads with deletion percentage = 0.47% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.5009X std coverageData = 20.6699X There is a 4.99% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 143666005 0.5763917635334598 30.022944452918978 chr2 243199373 105590172 0.43417123447929284 21.341624222383388 chr3 198022430 231631481 1.169723455065166 27.303644245938294 chr4 191154276 64307643 0.3364174966193275 13.89095508687568 chr5 180915260 86421646 0.47769130144134886 14.401057131902519 chr6 171115067 73766091 0.43109056550817937 14.027647621651518 chr7 159138663 61751783 0.3880375883263516 13.191101840935927 chr8 146364022 65014109 0.4441946054201763 15.280840096445486 chr9 141213431 84326448 0.5971560028167575 20.826154052760202 chr10 135534747 60117129 0.4435551054667922 24.236812102310264 chr11 135006516 70265089 0.5204570200152413 23.206890206950064 chr12 133851895 67352059 0.5031834551165675 20.33614478071332 chr13 115169878 39490942 0.3428929741507584 14.192516182919961 chr14 107349540 37244124 0.34694255792805445 12.408764043680971 chr15 102531392 41536718 0.40511220212439913 16.07600802012235 chr16 90354753 68704359 0.7603845588510435 40.97872593945558 chr17 81195210 51583721 0.635304976734465 15.150856798527036 chr18 78077248 27455107 0.3516403011540571 10.334664506226277 chr19 59128983 53146108 0.8988165414581881 36.112028411891444 chr20 63025520 25459820 0.40396049092494596 12.260311069969728 chr21 48129895 8462701 0.1758304479991074 8.300027135758949 chr22 51304566 9679277 0.1886630714311081 7.107076728232604 chrMT 16571 1774 0.1070544927886066 0.34758972749303385 chrX 155270560 65152643 0.4196071876085202 19.30453173609526 chrY 59373566 8638501 0.1454940570691004 9.40799691530708