BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,551,060 number of mapped reads = 20,809,721 (96.56%) number of supplementary alignments = 461,932 (2.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,445,925 number of mapped paired reads (second in pair) = 10,363,796 number of mapped paired reads (both in pair) = 20,368,656 number of mapped paired reads (singletons) = 441,065 number of mapped bases = 1,838,452,718 bp number of sequenced bases = 1,837,125,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,887,675 duplication rate = 7.19% >>>>>>> Insert size mean insert size = 211,074.3811 std insert size = 4,500,263.3606 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.8549 >>>>>>> ACTG content number of A's = 520,770,635 bp (28.35%) number of C's = 350,024,954 bp (19.05%) number of T's = 541,861,327 bp (29.5%) number of G's = 424,279,834 bp (23.09%) number of N's = 188,617 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 19,673,883 number of insertions = 299,561 mapped reads with insertion percentage = 1.42% number of deletions = 903,716 mapped reads with deletion percentage = 4.24% homopolymer indels = 51.44% >>>>>>> Coverage mean coverageData = 0.5939X std coverageData = 2.3314X There is a 29.22% of reference with a coverageData >= 1X There is a 13.56% of reference with a coverageData >= 2X There is a 6.59% of reference with a coverageData >= 3X There is a 3.56% of reference with a coverageData >= 4X There is a 2.02% of reference with a coverageData >= 5X There is a 1.21% of reference with a coverageData >= 6X There is a 0.76% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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% 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 149488576 0.5997520704271385 3.001898938766482 chr2 243199373 158806174 0.6529875963125941 3.8077031922716422 chr3 198022430 125072691 0.631608707155043 1.3484856853164005 chr4 191154276 116259792 0.6081987514629283 1.8961435199761094 chr5 180915260 114727592 0.6341509942279053 1.327692768261433 chr6 171115067 107273622 0.6269092715254584 1.394869982442958 chr7 159138663 96398768 0.6057532857367288 1.836421611674387 chr8 146364022 95329816 0.6513200081369723 1.5489143996701924 chr9 141213431 73595028 0.5211616733538611 2.5860126004683663 chr10 135534747 91375468 0.6741848125484751 5.050839342258424 chr11 135006516 88156725 0.6529812605489352 1.8566184176629077 chr12 133851895 84404789 0.6305834444854143 1.3402206697262056 chr13 115169878 57760366 0.5015232020997713 1.1781791011237208 chr14 107349540 55543229 0.5174053750020726 1.273260024571021 chr15 102531392 53394782 0.520765211107248 1.252991071766262 chr16 90354753 55963890 0.6193795914643251 3.3006391150690315 chr17 81195210 44812503 0.5519106730557135 1.8132575174469996 chr18 78077248 47174780 0.6042064904746642 2.581056221000848 chr19 59128983 28466500 0.4814305701824772 1.8463008029231265 chr20 63025520 42480688 0.6740236018679417 1.4839913805721199 chr21 48129895 22804975 0.4738214159827276 1.6490861444633438 chr22 51304566 21712888 0.42321550873269254 1.167114421654673 chrMT 16571 214630 12.952145314102951 8.913044241629013 chrX 155270560 103325587 0.6654551062352064 1.5421677399250528 chrY 59373566 3908859 0.06583500475615697 1.5994183055218463