BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927059.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 = 28,109,306 number of mapped reads = 27,541,804 (97.98%) number of supplementary alignments = 666,698 (2.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,825,200 number of mapped paired reads (second in pair) = 13,716,604 number of mapped paired reads (both in pair) = 27,227,258 number of mapped paired reads (singletons) = 314,546 number of mapped bases = 2,591,415,488 bp number of sequenced bases = 2,589,448,570 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,913,194 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 255,271.2792 std insert size = 4,997,723.113 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 53.0448 >>>>>>> ACTG content number of A's = 733,833,137 bp (28.34%) number of C's = 525,472,632 bp (20.29%) number of T's = 740,437,515 bp (28.59%) number of G's = 589,525,346 bp (22.77%) number of N's = 179,940 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 24,229,155 number of insertions = 446,307 mapped reads with insertion percentage = 1.59% number of deletions = 1,331,268 mapped reads with deletion percentage = 4.71% homopolymer indels = 52.22% >>>>>>> Coverage mean coverageData = 0.8371X std coverageData = 2.6595X There is a 33.13% of reference with a coverageData >= 1X There is a 18.41% of reference with a coverageData >= 2X There is a 10.7% of reference with a coverageData >= 3X There is a 6.64% of reference with a coverageData >= 4X There is a 4.27% of reference with a coverageData >= 5X There is a 2.83% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.33% of reference with a coverageData >= 8X There is a 0.94% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.01% 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 0.01% 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% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211033442 0.8466716799072689 2.860561194279226 chr2 243199373 222836047 0.9162690028810231 4.519501499419889 chr3 198022430 166328049 0.8399455001132953 1.75150599205717 chr4 191154276 137339127 0.718472690613523 2.0910105160678767 chr5 180915260 147721528 0.816523315943608 1.7248106808095984 chr6 171115067 141135940 0.824801360128036 1.7635120427972333 chr7 159138663 131210157 0.8245020696196247 2.072089358428944 chr8 146364022 125989855 0.8607979835372384 1.9577910796674742 chr9 141213431 112036504 0.7933841930375589 2.712514039880907 chr10 135534747 129511494 0.9555593444978356 4.30059877085899 chr11 135006516 127489272 0.9443193986281373 2.4946963035862706 chr12 133851895 122055364 0.911868778548111 2.042174757117671 chr13 115169878 72420553 0.6288150535333553 1.5327011572774778 chr14 107349540 82156112 0.7653140572376929 1.7498322595064428 chr15 102531392 90458318 0.8822499747199375 1.946474910147327 chr16 90354753 89579228 0.9914168876096645 4.150404078364317 chr17 81195210 79419086 0.978125261330071 2.209759067889258 chr18 78077248 69239945 0.8868133390152276 2.849666843023157 chr19 59128983 54554463 0.922634894633652 2.3047134258219844 chr20 63025520 67925709 1.077749283147525 2.17272147984233 chr21 48129895 32878543 0.683121020729424 2.1753388577178727 chr22 51304566 41337756 0.8057324956223194 2.023996034330666 chrMT 16571 2780454 167.79035664715468 117.90665011260526 chrX 155270560 129923991 0.8367586939855179 1.8399338692961484 chrY 59373566 4054551 0.06828882401976664 2.1944504237116633