BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124810.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 71,393,276 number of mapped reads = 71,330,973 (99.91%) number of supplementary alignments = 20,165 (0.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 35,668,230 number of mapped paired reads (second in pair) = 35,662,743 number of mapped paired reads (both in pair) = 71,301,464 number of mapped paired reads (singletons) = 29,509 number of mapped bases = 6,992,908,920 bp number of sequenced bases = 6,992,157,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,927,086 duplication rate = 40.94% >>>>>>> Insert size mean insert size = 102,806.2893 std insert size = 3,179,111.8661 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 56.4723 >>>>>>> ACTG content number of A's = 1,845,274,456 bp (26.39%) number of C's = 1,658,141,118 bp (23.71%) number of T's = 1,828,714,676 bp (26.15%) number of G's = 1,638,414,616 bp (23.43%) number of N's = 21,612,674 bp (0.31%) GC percentage = 47.15% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 38,691,336 number of insertions = 432,228 mapped reads with insertion percentage = 0.6% number of deletions = 333,779 mapped reads with deletion percentage = 0.46% homopolymer indels = 37.13% >>>>>>> Coverage mean coverageData = 2.2589X std coverageData = 15.2202X There is a 14.34% of reference with a coverageData >= 1X There is a 6.97% of reference with a coverageData >= 2X There is a 4.72% of reference with a coverageData >= 3X There is a 4.07% of reference with a coverageData >= 4X There is a 3.69% of reference with a coverageData >= 5X There is a 3.49% of reference with a coverageData >= 6X There is a 3.33% of reference with a coverageData >= 7X There is a 3.21% of reference with a coverageData >= 8X There is a 3.1% of reference with a coverageData >= 9X There is a 3.01% of reference with a coverageData >= 10X There is a 2.93% of reference with a coverageData >= 11X There is a 2.86% of reference with a coverageData >= 12X There is a 2.79% of reference with a coverageData >= 13X There is a 2.73% of reference with a coverageData >= 14X There is a 2.67% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.56% of reference with a coverageData >= 17X There is a 2.52% of reference with a coverageData >= 18X There is a 2.47% of reference with a coverageData >= 19X There is a 2.42% of reference with a coverageData >= 20X There is a 2.38% of reference with a coverageData >= 21X There is a 2.34% of reference with a coverageData >= 22X There is a 2.3% of reference with a coverageData >= 23X There is a 2.26% of reference with a coverageData >= 24X There is a 2.23% of reference with a coverageData >= 25X There is a 2.19% of reference with a coverageData >= 26X There is a 2.16% of reference with a coverageData >= 27X There is a 2.12% of reference with a coverageData >= 28X There is a 2.09% of reference with a coverageData >= 29X There is a 2.06% of reference with a coverageData >= 30X There is a 2.03% of reference with a coverageData >= 31X There is a 2% of reference with a coverageData >= 32X There is a 1.97% of reference with a coverageData >= 33X There is a 1.94% of reference with a coverageData >= 34X There is a 1.91% of reference with a coverageData >= 35X There is a 1.89% of reference with a coverageData >= 36X There is a 1.86% of reference with a coverageData >= 37X There is a 1.83% of reference with a coverageData >= 38X There is a 1.81% of reference with a coverageData >= 39X There is a 1.78% of reference with a coverageData >= 40X There is a 1.76% of reference with a coverageData >= 41X There is a 1.73% of reference with a coverageData >= 42X There is a 1.71% of reference with a coverageData >= 43X There is a 1.69% of reference with a coverageData >= 44X There is a 1.66% of reference with a coverageData >= 45X There is a 1.64% of reference with a coverageData >= 46X There is a 1.62% of reference with a coverageData >= 47X There is a 1.6% of reference with a coverageData >= 48X There is a 1.57% of reference with a coverageData >= 49X There is a 1.55% of reference with a coverageData >= 50X There is a 1.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 701181854 2.813159907834292 17.22224946682456 chr2 243199373 564282417 2.320246183364955 15.755974907097116 chr3 198022430 450414729 2.2745641945712918 15.45753785628543 chr4 191154276 324081325 1.6953914491559687 13.509920758546887 chr5 180915260 355973843 1.9676275124608062 14.55304670524549 chr6 171115067 399647496 2.3355482542048738 16.03908618629836 chr7 159138663 347394373 2.1829665176965825 15.04682007525328 chr8 146364022 261633242 1.787551601991369 13.431577578649627 chr9 141213431 279912692 1.9821959569837235 14.139623905251753 chr10 135534747 297553321 2.1954024896656206 15.027603985837155 chr11 135006516 408122541 3.0229840239711097 17.914278436647 chr12 133851895 381826400 2.852603618349968 17.02371628641839 chr13 115169878 151011198 1.3112039417112171 11.913772655922601 chr14 107349540 231795850 2.1592626293508106 14.972683986925261 chr15 102531392 244852568 2.388074161716248 15.674011125036357 chr16 90354753 251013488 2.77808836464862 16.323264689931268 chr17 81195210 351823019 4.333051407835511 20.38051909177808 chr18 78077248 121897405 1.5612410545002815 12.630080180259283 chr19 59128983 340805071 5.7637566842642975 23.12271549773575 chr20 63025520 165584830 2.6272663835221035 16.251150235883582 chr21 48129895 74811032 1.554356850352572 12.883980337811597 chr22 51304566 128430413 2.503294014805622 14.975223784537803 chrMT 16571 200429 12.09516625429968 28.948541518531677 chrX 155270560 148136400 0.9540533633677885 7.484434589350305 chrY 59373566 10522984 0.17723348467902367 2.7316046852285623