BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548925.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 = 5,615,372 number of mapped reads = 4,880,527 (86.91%) number of secondary alignments = 0 number of mapped bases = 193,190,385 bp number of sequenced bases = 193,168,176 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,966 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1702 >>>>>>> ACTG content number of A's = 57,225,975 bp (29.62%) number of C's = 39,319,303 bp (20.35%) number of T's = 57,390,482 bp (29.71%) number of G's = 39,230,705 bp (20.31%) number of N's = 1,711 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 538,678 number of insertions = 6,359 mapped reads with insertion percentage = 0.13% number of deletions = 16,646 mapped reads with deletion percentage = 0.34% homopolymer indels = 41.56% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.7676X There is a 5.42% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 15015470 0.06024245773092778 0.6494712949710529 chr2 243199373 16259967 0.06685858931059004 0.3769154792057366 chr3 198022430 13191899 0.06661820582648137 0.28847241465218487 chr4 191154276 12894748 0.06745728251456955 0.29397547833562193 chr5 180915260 12213489 0.06750944613516847 0.29411269386709477 chr6 171115067 11417735 0.06672548011216335 0.3151165116990096 chr7 159138663 10789060 0.06779659824086871 0.5327166387937057 chr8 146364022 10296374 0.070347711543483 3.0774240513052455 chr9 141213431 8156960 0.05776334405471672 0.35670362256097005 chr10 135534747 8855100 0.06533453742308605 0.34528234725021123 chr11 135006516 8757813 0.06486955785156326 0.4064767585917053 chr12 133851895 8814707 0.06585418159376824 0.29518663544857543 chr13 115169878 6456747 0.05606281010387108 0.26242067943281666 chr14 107349540 5915735 0.05510722262992464 0.2867029123488553 chr15 102531392 5532854 0.05396253666389314 0.258939098831796 chr16 90354753 5114407 0.056603629916402956 0.28214698499502544 chr17 81195210 4841529 0.0596282588591125 0.29072118070825714 chr18 78077248 5163933 0.06613876810822021 0.6110238169381069 chr19 59128983 3501107 0.059211351563411806 0.5934391443867033 chr20 63025520 3750039 0.05950032621706255 0.2787214307102331 chr21 48129895 2469922 0.051317834788544625 0.2769276073803575 chr22 51304566 2003190 0.03904506277277543 0.24439202833271112 chrMT 16571 5181 0.31265463761993845 0.6306992306142752 chrX 155270560 11224060 0.07228710967487977 0.34671512649696157 chrY 59373566 548359 0.009235743057777598 0.13373918316807087