BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975216.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 56,199,150 number of mapped reads = 56,028,873 (99.7%) number of supplementary alignments = 145,323 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,047,466 number of mapped paired reads (second in pair) = 27,981,407 number of mapped paired reads (both in pair) = 55,920,366 number of mapped paired reads (singletons) = 108,507 number of mapped bases = 5,497,698,805 bp number of sequenced bases = 5,495,572,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,271,340 duplication rate = 37.37% >>>>>>> Insert size mean insert size = 170,916.4864 std insert size = 4,239,833.5417 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 55.629 >>>>>>> ACTG content number of A's = 1,458,174,496 bp (26.53%) number of C's = 1,257,727,489 bp (22.89%) number of T's = 1,473,633,544 bp (26.81%) number of G's = 1,305,623,256 bp (23.76%) number of N's = 413,308 bp (0.01%) GC percentage = 46.64% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 33,618,976 number of insertions = 460,648 mapped reads with insertion percentage = 0.81% number of deletions = 1,356,713 mapped reads with deletion percentage = 2.38% homopolymer indels = 49.13% >>>>>>> Coverage mean coverageData = 1.7759X std coverageData = 26.092X There is a 16.49% of reference with a coverageData >= 1X There is a 8% of reference with a coverageData >= 2X There is a 4.55% of reference with a coverageData >= 3X There is a 3.2% of reference with a coverageData >= 4X There is a 2.48% of reference with a coverageData >= 5X There is a 2.1% of reference with a coverageData >= 6X There is a 1.87% of reference with a coverageData >= 7X There is a 1.71% of reference with a coverageData >= 8X There is a 1.6% of reference with a coverageData >= 9X There is a 1.51% of reference with a coverageData >= 10X There is a 1.44% of reference with a coverageData >= 11X There is a 1.39% of reference with a coverageData >= 12X There is a 1.33% of reference with a coverageData >= 13X There is a 1.29% of reference with a coverageData >= 14X There is a 1.25% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.18% of reference with a coverageData >= 17X There is a 1.15% of reference with a coverageData >= 18X There is a 1.12% of reference with a coverageData >= 19X There is a 1.09% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 1.04% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.97% of reference with a coverageData >= 25X There is a 0.95% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.92% of reference with a coverageData >= 28X There is a 0.9% of reference with a coverageData >= 29X There is a 0.88% of reference with a coverageData >= 30X There is a 0.87% of reference with a coverageData >= 31X There is a 0.85% of reference with a coverageData >= 32X There is a 0.84% of reference with a coverageData >= 33X There is a 0.82% of reference with a coverageData >= 34X There is a 0.81% of reference with a coverageData >= 35X There is a 0.8% of reference with a coverageData >= 36X There is a 0.78% of reference with a coverageData >= 37X There is a 0.77% of reference with a coverageData >= 38X There is a 0.76% of reference with a coverageData >= 39X There is a 0.75% of reference with a coverageData >= 40X There is a 0.74% of reference with a coverageData >= 41X There is a 0.73% of reference with a coverageData >= 42X There is a 0.72% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.68% of reference with a coverageData >= 46X There is a 0.68% of reference with a coverageData >= 47X There is a 0.67% of reference with a coverageData >= 48X There is a 0.66% of reference with a coverageData >= 49X There is a 0.65% of reference with a coverageData >= 50X There is a 0.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 848876106 3.4057131035192083 41.435287038189216 chr2 243199373 436428895 1.7945313329405663 24.384460081116973 chr3 198022430 421401710 2.1280503930792083 30.17480201609659 chr4 191154276 230415947 1.205392585620214 19.55048276060903 chr5 180915260 193533986 1.0697493732701155 17.170469889330136 chr6 171115067 319518517 1.8672728392760412 27.61198185501664 chr7 159138663 256096355 1.6092654680654193 24.751406655348973 chr8 146364022 205368039 1.4031319732386147 21.556911764966898 chr9 141213431 288939524 2.0461192816708773 29.029835768692635 chr10 135534747 199052803 1.4686477630714136 22.030743326688143 chr11 135006516 256422617 1.899335118017563 25.684745906740346 chr12 133851895 218060351 1.6291166516544275 22.212323608388722 chr13 115169878 69826986 0.6062955628033225 12.871743836946981 chr14 107349540 124329751 1.158176839882127 19.240102703225077 chr15 102531392 132925625 1.2964383142286804 18.342495914517276 chr16 90354753 156834483 1.7357635076485682 23.066293052110563 chr17 81195210 259867076 3.200522247556229 36.18269200461544 chr18 78077248 130636047 1.6731640823201146 23.49555049358822 chr19 59128983 233312523 3.9458233705795345 44.365661963056255 chr20 63025520 139464438 2.212824868402514 27.484351139518637 chr21 48129895 70367103 1.4620248600168357 22.533556624025923 chr22 51304566 65157499 1.2700136475182346 18.41132426489011 chrMT 16571 110186 6.649327137770804 10.591937827219533 chrX 155270560 231914426 1.493614926100608 24.48387577648205 chrY 59373566 8837812 0.14885095498559073 4.02734914161555