BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084276.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 = 3,348,603 number of mapped reads = 3,033,604 (90.59%) number of supplementary alignments = 22,851 (0.68%) number of secondary alignments = 0 number of mapped bases = 199,586,217 bp number of sequenced bases = 199,519,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,695 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0497 >>>>>>> ACTG content number of A's = 55,523,176 bp (27.83%) number of C's = 38,828,580 bp (19.46%) number of T's = 60,480,907 bp (30.31%) number of G's = 44,424,421 bp (22.27%) number of N's = 262,652 bp (0.13%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,063,266 number of insertions = 14,963 mapped reads with insertion percentage = 0.49% number of deletions = 41,494 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.0645X std coverageData = 0.4038X There is a 5.36% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 19811991 0.07948622523191226 0.713001417821167 chr2 243199373 19198556 0.07894163444245393 0.47110213603040885 chr3 198022430 13139413 0.06635315504410283 0.3030609632304903 chr4 191154276 9326809 0.04879205004025126 0.2653986537329802 chr5 180915260 10415675 0.05757211967636119 0.27708224383487046 chr6 171115067 9991323 0.05838949880433381 0.33116381891849056 chr7 159138663 10921259 0.06862731402990359 0.5260883489039834 chr8 146364022 9307876 0.06359401629452353 0.3580344264918903 chr9 141213431 7394820 0.05236626535899407 0.32453008998022487 chr10 135534747 14363593 0.10597720007549061 0.5589780465829316 chr11 135006516 10755551 0.07966690289230188 0.39718418836349595 chr12 133851895 10327661 0.07715737606852709 0.3236343502207885 chr13 115169878 4768959 0.041408040737874185 0.23656518196335966 chr14 107349540 5604190 0.05220506766959598 0.2731373427820556 chr15 102531392 4446009 0.043362417239005205 0.25320320068215524 chr16 90354753 4110227 0.04548988142328274 0.2719775989235668 chr17 81195210 5465309 0.06731073175375739 0.3190974200265683 chr18 78077248 5130016 0.06570436498991358 0.5023754147282158 chr19 59128983 4193334 0.07091841914480417 0.5075945655223328 chr20 63025520 4135935 0.06562317930895295 0.30241281154589406 chr21 48129895 2057078 0.04274013064021852 0.24905031732886504 chr22 51304566 1758206 0.03426997121464784 0.21189224567963608 chrMT 16571 14442 0.8715225393760183 1.1503233058858633 chrX 155270560 12531212 0.08070565340912018 0.36376509233530185 chrY 59373566 416773 0.007019504268953629 0.13094158541335685