BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926913.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 = 28,728,954 number of mapped reads = 26,392,500 (91.87%) number of supplementary alignments = 386,491 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,250,565 number of mapped paired reads (second in pair) = 13,141,935 number of mapped paired reads (both in pair) = 26,024,426 number of mapped paired reads (singletons) = 368,074 number of mapped bases = 2,458,829,877 bp number of sequenced bases = 2,457,001,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,868,943 duplication rate = 5.7% >>>>>>> Insert size mean insert size = 159,283.749 std insert size = 3,958,967.9718 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.0511 >>>>>>> ACTG content number of A's = 690,312,098 bp (28.1%) number of C's = 499,818,591 bp (20.34%) number of T's = 696,922,919 bp (28.36%) number of G's = 569,717,998 bp (23.19%) number of N's = 230,012 bp (0.01%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 25,095,430 number of insertions = 389,410 mapped reads with insertion percentage = 1.45% number of deletions = 1,268,003 mapped reads with deletion percentage = 4.68% homopolymer indels = 52.51% >>>>>>> Coverage mean coverageData = 0.7943X std coverageData = 2.7676X There is a 31.78% of reference with a coverageData >= 1X There is a 17.37% of reference with a coverageData >= 2X There is a 10% of reference with a coverageData >= 3X There is a 6.21% of reference with a coverageData >= 4X There is a 4% of reference with a coverageData >= 5X There is a 2.67% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.26% of reference with a coverageData >= 8X There is a 0.89% of reference with a coverageData >= 9X There is a 0.64% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% 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 0.02% 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% 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 206622531 0.8289749897955119 2.4646508277592196 chr2 243199373 229822808 0.9449975350059805 3.89670472529932 chr3 198022430 166022186 0.8384009124622902 1.7594043871758263 chr4 191154276 136641312 0.7148221575749631 1.7934449214271142 chr5 180915260 138874396 0.7676212388053943 1.6554824540266513 chr6 171115067 134984248 0.788850744511002 1.6784422941256338 chr7 159138663 120549945 0.7575151300598774 1.8411678799246471 chr8 146364022 120914669 0.8261228910476374 1.8752822843677137 chr9 141213431 105725617 0.7486937768688589 3.1460623375378103 chr10 135534747 120064567 0.8858581998902466 6.913115316907553 chr11 135006516 115694136 0.8569522377719903 2.0935212043834066 chr12 133851895 109445083 0.8176580764881961 1.7825974957172466 chr13 115169878 71107490 0.6174139561040431 1.4824635632764922 chr14 107349540 70435710 0.656134250784866 1.5849874224007086 chr15 102531392 71341642 0.69580292053384 1.6845877900776498 chr16 90354753 114499395 1.2672204969671048 5.516143961138749 chr17 81195210 67776253 0.8347321596926716 1.9779320711707984 chr18 78077248 64443188 0.8253772981342785 3.2263598036188905 chr19 59128983 22239430 0.37611724186089923 1.4180892862970091 chr20 63025520 58764868 0.9323979873549635 1.97944967794696 chr21 48129895 31059623 0.64532912444542 2.3338989483589896 chr22 51304566 49035968 0.955781752446751 2.277026774387889 chrMT 16571 40942 2.4707018284955646 2.6153523780782932 chrX 155270560 128744831 0.8291644662066009 1.8366347365321203 chrY 59373566 3979039 0.06701701225087273 1.6365026979345514