BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124938.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 = 2,010,204 number of mapped reads = 1,973,647 (98.18%) number of supplementary alignments = 34,164 (1.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 988,592 number of mapped paired reads (second in pair) = 985,055 number of mapped paired reads (both in pair) = 1,964,922 number of mapped paired reads (singletons) = 8,725 number of mapped bases = 263,190,162 bp number of sequenced bases = 262,962,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,673 duplication rate = 15.34% >>>>>>> Insert size mean insert size = 78,496.1998 std insert size = 2,625,894.7578 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.3809 >>>>>>> ACTG content number of A's = 76,440,687 bp (29.07%) number of C's = 53,265,777 bp (20.26%) number of T's = 77,058,411 bp (29.3%) number of G's = 56,172,393 bp (21.36%) number of N's = 24,812 bp (0.01%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 2,961,065 number of insertions = 59,399 mapped reads with insertion percentage = 2.77% number of deletions = 104,640 mapped reads with deletion percentage = 5.04% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.085X std coverageData = 1.1021X There is a 4.77% of reference with a coverageData >= 1X There is a 2.65% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 22549423 0.09046887389700826 0.995737698423849 chr2 243199373 22645427 0.09311466029149672 1.6284992174624597 chr3 198022430 16589744 0.08377709535227904 0.41117592699210614 chr4 191154276 16374779 0.08566263513770417 0.9561697009650982 chr5 180915260 13793846 0.076244789964097 0.402753559541601 chr6 171115067 11192252 0.06540775278427119 0.6128409074141549 chr7 159138663 25750607 0.16181238747745416 2.17275580709368 chr8 146364022 21061507 0.14389811589080273 0.59500415036299 chr9 141213431 9945205 0.07042676415106719 1.5602443115300246 chr10 135534747 14421770 0.10640644055653123 2.087925238017735 chr11 135006516 11536665 0.08545265326304695 0.6922385127445222 chr12 133851895 13182879 0.09848854960178188 0.4447032353420621 chr13 115169878 5182382 0.044997720671372074 0.2961501719697808 chr14 107349540 6949494 0.0647370636148045 0.4014515222346401 chr15 102531392 6317644 0.06161668028460981 0.3453350298282186 chr16 90354753 7305642 0.08085509347803761 1.501368545875118 chr17 81195210 6380907 0.0785872343947383 0.9896952331104506 chr18 78077248 6031017 0.0772442312515933 1.4688443913124396 chr19 59128983 3625994 0.061323462979229665 0.579888185551343 chr20 63025520 5345174 0.08480967709588116 0.5007620128509838 chr21 48129895 3273660 0.06801718557665667 0.5727627313993734 chr22 51304566 2564227 0.04998048321858916 0.3450621423742031 chrMT 16571 116625 7.03789753183272 4.63732165004512 chrX 155270560 7621320 0.04908412773161892 0.37609920069034725 chrY 59373566 3431972 0.057803029718646176 1.6553011831343496