BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038398.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,327,614 number of mapped reads = 14,027,601 (97.91%) number of supplementary alignments = 219,715 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,073,277 number of mapped paired reads (second in pair) = 6,954,324 number of mapped paired reads (both in pair) = 13,893,284 number of mapped paired reads (singletons) = 134,317 number of mapped bases = 2,025,946,263 bp number of sequenced bases = 2,024,565,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,038,301 duplication rate = 9.38% >>>>>>> Insert size mean insert size = 74,071.773 std insert size = 2,541,088.3222 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.7783 >>>>>>> ACTG content number of A's = 595,895,495 bp (29.43%) number of C's = 411,973,754 bp (20.35%) number of T's = 593,873,411 bp (29.33%) number of G's = 422,778,921 bp (20.88%) number of N's = 44,325 bp (0%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 27,311,916 number of insertions = 355,819 mapped reads with insertion percentage = 2.41% number of deletions = 713,399 mapped reads with deletion percentage = 4.9% homopolymer indels = 48.06% >>>>>>> Coverage mean coverageData = 0.6544X std coverageData = 9.5682X There is a 26.93% of reference with a coverageData >= 1X There is a 14.67% of reference with a coverageData >= 2X There is a 7.73% of reference with a coverageData >= 3X There is a 4.56% of reference with a coverageData >= 4X There is a 2.64% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 0.99% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 134386808 0.5391633828667572 15.861202736435477 chr2 243199373 180067737 0.7404120116707702 8.901650005440503 chr3 198022430 139150179 0.7026990780791853 1.4717825959380801 chr4 191154276 123480878 0.6459749715460197 7.684823638370669 chr5 180915260 124321211 0.6871792407119223 1.6004861391158436 chr6 171115067 117911064 0.6890747031645086 15.085657401702724 chr7 159138663 152025623 0.9553028794768749 10.95381162684298 chr8 146364022 95638148 0.6534266187355797 2.644504285146669 chr9 141213431 87371497 0.6187194545255401 16.524356941276054 chr10 135534747 85535531 0.6310966958163134 14.445033622449008 chr11 135006516 95655712 0.7085266314108869 8.683952919438214 chr12 133851895 73746178 0.5509535595293589 1.35338697496033 chr13 115169878 141739329 1.230697917384266 2.250002121304596 chr14 107349540 39807732 0.370823498638187 1.1999479809783824 chr15 102531392 38078464 0.3713834685868695 1.0178869152536039 chr16 90354753 73265382 0.8108636188734863 12.241783852602497 chr17 81195210 52284941 0.6439412004722939 10.122488553379828 chr18 78077248 34541362 0.4423998397074651 13.567565748278078 chr19 59128983 28943166 0.4894920313444255 9.36453521523196 chr20 63025520 68870148 1.0927343082611616 3.0777256833035747 chr21 48129895 18647617 0.3874435421062107 3.552204888582866 chr22 51304566 13529595 0.263711323471677 0.8848848582710421 chrMT 16571 1699365 102.550540100175 73.95389238357944 chrX 155270560 77922069 0.5018470275369652 2.4317918412745287 chrY 59373566 27326527 0.46024735991097454 11.701099234890613