BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926960.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 = 14,218,966 number of mapped reads = 13,708,091 (96.41%) number of supplementary alignments = 347,906 (2.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,865,636 number of mapped paired reads (second in pair) = 6,842,455 number of mapped paired reads (both in pair) = 13,475,708 number of mapped paired reads (singletons) = 232,383 number of mapped bases = 1,262,202,007 bp number of sequenced bases = 1,261,238,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 979,703 duplication rate = 5.77% >>>>>>> Insert size mean insert size = 287,254.7477 std insert size = 5,289,460.4285 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 50.3884 >>>>>>> ACTG content number of A's = 361,234,134 bp (28.64%) number of C's = 247,707,419 bp (19.64%) number of T's = 364,361,544 bp (28.89%) number of G's = 287,864,194 bp (22.82%) number of N's = 70,982 bp (0.01%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 12,635,089 number of insertions = 213,009 mapped reads with insertion percentage = 1.53% number of deletions = 667,700 mapped reads with deletion percentage = 4.74% homopolymer indels = 52.92% >>>>>>> Coverage mean coverageData = 0.4077X std coverageData = 2.0426X There is a 20.94% of reference with a coverageData >= 1X There is a 9.61% of reference with a coverageData >= 2X There is a 4.56% of reference with a coverageData >= 3X There is a 2.34% of reference with a coverageData >= 4X There is a 1.23% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 114222475 0.458263552330327 2.3376942177881417 chr2 243199373 115407986 0.4745406395435074 2.8033099117364637 chr3 198022430 89711977 0.4530394713366562 1.103234979849077 chr4 191154276 81035566 0.42392756100313445 1.6703641938808818 chr5 180915260 80876512 0.4470408521647096 1.0949761941608382 chr6 171115067 78248775 0.45728746376261536 1.9418537697830431 chr7 159138663 69390023 0.4360349753598219 1.1549192947741407 chr8 146364022 69938379 0.4778385975209126 1.174169007292717 chr9 141213431 55784446 0.3950364041505372 1.4417646806594124 chr10 135534747 64534479 0.47614711672424487 3.7248269959385567 chr11 135006516 64710773 0.4793159242773141 1.3550894206375983 chr12 133851895 62679784 0.46827715065221903 5.237777011271759 chr13 115169878 591048 0.005131966884605018 0.1452676410909114 chr14 107349540 39826062 0.37099424925342017 1.0023100972899466 chr15 102531392 696530 0.006793334084452886 0.3092219586601744 chr16 90354753 38319456 0.42410005813418583 1.1503073390860947 chr17 81195210 35238189 0.43399344616511243 1.1424282403763502 chr18 78077248 35789071 0.4583802825632379 1.5427240855467532 chr19 59128983 21788038 0.3684832191346839 1.4831570583994946 chr20 63025520 30611699 0.48570323576862195 1.1987468882039494 chr21 48129895 17060939 0.3544769628107437 2.530487556981798 chr22 51304566 17230235 0.3358421353764107 0.9703682819056026 chrMT 16571 139716 8.431355983344396 9.672246460634371 chrX 155270560 76518126 0.49280511386060566 1.2874533822169756 chrY 59373566 1851723 0.031187666915610222 1.1465751647679285