BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082484.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,027,507 number of mapped reads = 1,813,344 (89.44%) number of supplementary alignments = 15,634 (0.77%) number of secondary alignments = 0 number of mapped bases = 124,596,217 bp number of sequenced bases = 124,550,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,046 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8341 >>>>>>> ACTG content number of A's = 36,059,643 bp (28.95%) number of C's = 23,274,634 bp (18.69%) number of T's = 38,177,501 bp (30.65%) number of G's = 27,036,421 bp (21.71%) number of N's = 2,569 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,046,781 number of insertions = 10,142 mapped reads with insertion percentage = 0.56% number of deletions = 27,578 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3651X There is a 3.61% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9770844 0.03920088126881738 0.652466121350099 chr2 243199373 10785983 0.04435037338685902 0.41686965189284536 chr3 198022430 8548092 0.04316729170528813 0.22496589667816172 chr4 191154276 8454122 0.04422669571880254 0.2369144604026915 chr5 180915260 7799114 0.043109210356273985 0.2253446222600618 chr6 171115067 7480834 0.04371814902775335 0.2707100184838667 chr7 159138663 6889074 0.043289756682196076 0.4617368443590072 chr8 146364022 6486177 0.044315378269667936 0.6078842347401588 chr9 141213431 5265545 0.037287848349212616 0.3289397651128954 chr10 135534747 5845184 0.04312683005192757 0.3422521093930532 chr11 135006516 5536486 0.04100902803832076 0.2987362985300059 chr12 133851895 5624704 0.04202184810308438 0.22603547028984058 chr13 115169878 4109300 0.035680336485204925 0.20352292600441363 chr14 107349540 3801530 0.035412634278637806 0.2254808809416936 chr15 102531392 3431802 0.03347074425752456 0.19913341702501774 chr16 90354753 3308780 0.0366198776504873 0.23238745767454225 chr17 81195210 3021104 0.03720790918577586 0.22663859559860303 chr18 78077248 3404523 0.043604546615167585 0.5865572303966001 chr19 59128983 2191379 0.03706099595861474 0.5104173958686695 chr20 63025520 2410052 0.03823930369793062 0.21622144058302975 chr21 48129895 1644955 0.03417740678636427 0.21265552572396523 chr22 51304566 1216192 0.023705336480187748 0.1654649840861754 chrMT 16571 3880 0.23414398648240903 0.5406305245639438 chrX 155270560 7263843 0.046781843254767676 0.2597401298186926 chrY 59373566 302718 0.0050985315586400855 0.12560714719687077