BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975267.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 = 77,895,866 number of mapped reads = 77,748,178 (99.81%) number of supplementary alignments = 144,884 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,887,570 number of mapped paired reads (second in pair) = 38,860,608 number of mapped paired reads (both in pair) = 77,685,212 number of mapped paired reads (singletons) = 62,966 number of mapped bases = 7,261,765,664 bp number of sequenced bases = 7,259,379,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,671,096 duplication rate = 50.09% >>>>>>> Insert size mean insert size = 62,106.0506 std insert size = 2,457,504.1721 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 56.3116 >>>>>>> ACTG content number of A's = 1,903,003,651 bp (26.21%) number of C's = 1,668,986,702 bp (22.99%) number of T's = 1,912,062,037 bp (26.34%) number of G's = 1,775,011,652 bp (24.45%) number of N's = 315,236 bp (0%) GC percentage = 47.44% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 45,156,391 number of insertions = 670,894 mapped reads with insertion percentage = 0.85% number of deletions = 1,676,298 mapped reads with deletion percentage = 2.12% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 2.3458X std coverageData = 32.1831X There is a 11.01% of reference with a coverageData >= 1X There is a 5.64% of reference with a coverageData >= 2X There is a 3.56% of reference with a coverageData >= 3X There is a 2.82% of reference with a coverageData >= 4X There is a 2.39% of reference with a coverageData >= 5X There is a 2.17% of reference with a coverageData >= 6X There is a 2.01% of reference with a coverageData >= 7X There is a 1.89% of reference with a coverageData >= 8X There is a 1.8% of reference with a coverageData >= 9X There is a 1.73% of reference with a coverageData >= 10X There is a 1.67% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.57% of reference with a coverageData >= 13X There is a 1.53% of reference with a coverageData >= 14X There is a 1.49% of reference with a coverageData >= 15X There is a 1.45% of reference with a coverageData >= 16X There is a 1.42% of reference with a coverageData >= 17X There is a 1.39% of reference with a coverageData >= 18X There is a 1.36% of reference with a coverageData >= 19X There is a 1.33% of reference with a coverageData >= 20X There is a 1.31% of reference with a coverageData >= 21X There is a 1.28% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.24% of reference with a coverageData >= 24X There is a 1.22% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.18% of reference with a coverageData >= 27X There is a 1.16% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.12% of reference with a coverageData >= 30X There is a 1.11% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 1.08% of reference with a coverageData >= 33X There is a 1.06% of reference with a coverageData >= 34X There is a 1.05% of reference with a coverageData >= 35X There is a 1.03% of reference with a coverageData >= 36X There is a 1.02% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 0.99% of reference with a coverageData >= 39X There is a 0.98% of reference with a coverageData >= 40X There is a 0.97% of reference with a coverageData >= 41X There is a 0.96% of reference with a coverageData >= 42X There is a 0.95% of reference with a coverageData >= 43X There is a 0.94% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.91% of reference with a coverageData >= 46X There is a 0.9% of reference with a coverageData >= 47X There is a 0.89% of reference with a coverageData >= 48X There is a 0.88% of reference with a coverageData >= 49X There is a 0.87% of reference with a coverageData >= 50X There is a 0.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 835373886 3.3515418443029676 40.233942847898945 chr2 243199373 491213204 2.019796342155866 26.874923289705265 chr3 198022430 439159901 2.2177280674719526 31.308045936771155 chr4 191154276 285576520 1.4939583145919269 22.84731806473822 chr5 180915260 325982925 1.8018542216947315 27.18529833605913 chr6 171115067 679951232 3.9736491001110967 53.89606884268286 chr7 159138663 360190868 2.2633774923696577 32.45641927866166 chr8 146364022 236155641 1.613481494789751 23.93617809023414 chr9 141213431 296912828 2.102582069548328 29.40956790417466 chr10 135534747 301944445 2.22780100072788 29.31326016075508 chr11 135006516 349250235 2.5869139160660954 31.47093269372971 chr12 133851895 396185159 2.959877101478466 34.816389468912185 chr13 115169878 130368507 1.1319670495787102 21.087087015200936 chr14 107349540 232751483 2.168164698237179 28.49687173978273 chr15 102531392 258905670 2.5251356189526812 31.45708970532741 chr16 90354753 257312658 2.8478043429547086 34.09549055385312 chr17 81195210 334293798 4.117161566550539 42.121149625362406 chr18 78077248 116535827 1.4925708831335858 24.571606129043964 chr19 59128983 346317754 5.856988171097075 50.41640076356243 chr20 63025520 188015541 2.9831652479820874 37.27818654625261 chr21 48129895 67329698 1.398916369960915 22.735739984075526 chr22 51304566 156330007 3.047097348021617 35.29969876338687 chrMT 16571 106003 6.396898195642991 15.53730035092285 chrX 155270560 162242143 1.0448995804484764 17.433756424481523 chrY 59373566 13359731 0.2250114301707935 7.824648890978142