BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548953.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,187,648 number of mapped reads = 7,959,691 (86.63%) number of secondary alignments = 0 number of mapped bases = 315,415,741 bp number of sequenced bases = 315,382,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,375 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5324 >>>>>>> ACTG content number of A's = 90,788,676 bp (28.79%) number of C's = 66,114,350 bp (20.96%) number of T's = 91,976,675 bp (29.16%) number of G's = 66,502,688 bp (21.09%) number of N's = 455 bp (0%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 745,456 number of insertions = 9,007 mapped reads with insertion percentage = 0.11% number of deletions = 24,538 mapped reads with deletion percentage = 0.31% homopolymer indels = 42.43% >>>>>>> Coverage mean coverageData = 0.1019X std coverageData = 1.1077X There is a 7.49% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% 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 25632103 0.10283666655338042 1.2626942614633165 chr2 243199373 27114942 0.11149264763935061 0.5733438723603642 chr3 198022430 21753525 0.10985384332471831 0.42707612332913686 chr4 191154276 20479034 0.10713353856651368 0.44086496365641176 chr5 180915260 20060367 0.11088266959901558 0.432663954313577 chr6 171115067 18244622 0.10662194931086928 0.43814905583142844 chr7 159138663 17870067 0.1122924288989408 0.9793267262446406 chr8 146364022 16881613 0.11533990914789155 4.193745924161878 chr9 141213431 13622882 0.09647015799793152 0.5388631532020707 chr10 135534747 15295980 0.11285652084479857 0.55612615017693 chr11 135006516 14308229 0.10598176609490463 0.5590818664369435 chr12 133851895 14439089 0.1078736240529131 0.4326276657536557 chr13 115169878 10610910 0.0921326842075842 0.3879919550090299 chr14 107349540 10084272 0.09393866056622134 0.4542802110400464 chr15 102531392 9067845 0.08843969464493372 0.379095134873039 chr16 90354753 9030899 0.09994935186198782 0.4357864121274906 chr17 81195210 8559264 0.10541587367038031 0.43563169362674026 chr18 78077248 8442876 0.1081349076237933 0.9639405009614249 chr19 59128983 6067691 0.10261788199536596 1.056981358372637 chr20 63025520 6539628 0.10376158736968771 0.42939831437547904 chr21 48129895 4214198 0.08755884466400768 0.4597694500378004 chr22 51304566 3679865 0.07172587718605787 0.49105293997215427 chrMT 16571 33683 2.032647396053346 2.7654878138949353 chrX 155270560 10349476 0.06665446431055572 0.40325824870998206 chrY 59373566 3032681 0.05107796624511319 0.5576218750341141