BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548942.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 = 8,834,435 number of mapped reads = 7,697,307 (87.13%) number of secondary alignments = 0 number of mapped bases = 304,408,481 bp number of sequenced bases = 304,375,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,059 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.3783 >>>>>>> ACTG content number of A's = 88,524,737 bp (29.08%) number of C's = 63,912,539 bp (21%) number of T's = 88,587,344 bp (29.1%) number of G's = 63,348,083 bp (20.81%) number of N's = 2,581 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 937,513 number of insertions = 10,614 mapped reads with insertion percentage = 0.14% number of deletions = 25,283 mapped reads with deletion percentage = 0.33% homopolymer indels = 39.85% >>>>>>> Coverage mean coverageData = 0.0983X std coverageData = 1.1689X There is a 8.07% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 23959464 0.09612599520865386 1.3080337491806309 chr2 243199373 25433319 0.10457806155610443 0.6554878951136448 chr3 198022430 20553237 0.10379246936824278 0.3789220408818114 chr4 191154276 20023587 0.10475092380355645 0.3989545305408483 chr5 180915260 18828246 0.10407218274456229 0.39132675154407004 chr6 171115067 17867373 0.1044172983317711 0.44860808828930926 chr7 159138663 17023961 0.10697564425308764 1.0130919022960776 chr8 146364022 15887765 0.10854966120020944 4.427378147384791 chr9 141213431 12749582 0.090285902054175 0.6482331312487695 chr10 135534747 13969783 0.10307159831124339 0.5951845338757593 chr11 135006516 13782175 0.10208525787007199 0.6714342932624797 chr12 133851895 13902747 0.10386664305350328 0.4037799027351844 chr13 115169878 9937538 0.08628591236330041 0.33721155802033115 chr14 107349540 9340738 0.08701237098920032 0.4294499690234596 chr15 102531392 8599458 0.0838714644584168 0.3373692467946609 chr16 90354753 8368780 0.09262135883432718 0.4214876316751866 chr17 81195210 7935396 0.09773231696795907 0.40545023660765206 chr18 78077248 8016660 0.10267600620349733 1.2477550975385168 chr19 59128983 6250711 0.10571314916747342 1.2348339298354793 chr20 63025520 5990563 0.09504979887512233 0.387758649873183 chr21 48129895 3831481 0.07960709243184512 0.4026779606873637 chr22 51304566 3362936 0.06554847379471058 0.3397201297507543 chrMT 16571 12836 0.774606239816547 1.2045403791222695 chrX 155270560 17738302 0.11424124444453604 0.5260193433343352 chrY 59373566 1041843 0.017547253267556812 0.2277255916981966