BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240186.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,036,916 number of mapped reads = 823,471 (79.42%) number of supplementary alignments = 7,796 (0.75%) number of secondary alignments = 0 number of mapped bases = 55,381,626 bp number of sequenced bases = 55,354,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,845 duplication rate = 6.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0797 >>>>>>> ACTG content number of A's = 15,854,779 bp (28.64%) number of C's = 10,256,480 bp (18.53%) number of T's = 17,564,713 bp (31.73%) number of G's = 11,633,199 bp (21.02%) number of N's = 45,597 bp (0.08%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 506,967 number of insertions = 3,885 mapped reads with insertion percentage = 0.47% number of deletions = 15,311 mapped reads with deletion percentage = 1.84% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.0179X std coverageData = 0.2472X There is a 1.09% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 4333231 0.01738503592334079 0.3490947961688967 chr2 243199373 5732004 0.023569156158967566 0.27439358785659446 chr3 198022430 3449590 0.01742019830783816 0.2044324277946708 chr4 191154276 3656987 0.01913107609478744 0.2168380632562208 chr5 180915260 3089112 0.01707491120428426 0.20560743003800158 chr6 171115067 2958191 0.017287729548678493 0.22775588472663094 chr7 159138663 3211022 0.02017751022578341 0.28069225843582596 chr8 146364022 3179195 0.021721150844023675 0.36571891779040233 chr9 141213431 2063373 0.014611733355589952 0.21441031870119434 chr10 135534747 2610679 0.019262064214426135 0.24966483913580975 chr11 135006516 2450017 0.018147398159656235 0.23359499216030832 chr12 133851895 2720505 0.02032474026609784 0.2214787072320637 chr13 115169878 1582069 0.013736829694306006 0.18609981040788812 chr14 107349540 1786579 0.016642633028516006 0.204280232616745 chr15 102531392 1548802 0.01510563711063242 0.1929371033231945 chr16 90354753 1651538 0.01827837435403094 0.212980362635567 chr17 81195210 1290288 0.015891183728695326 0.19340884367900796 chr18 78077248 1355107 0.017355978018077686 0.32098096584786123 chr19 59128983 910891 0.015405152495181594 0.25070961402584957 chr20 63025520 1080692 0.01714689541633294 0.20005928671903037 chr21 48129895 838548 0.01742260189846664 0.20181848416692322 chr22 51304566 501964 0.00978400246091157 0.14849582093448188 chrMT 16571 10908 0.6582584032345664 1.083964560728571 chrX 155270560 3211399 0.020682600745434293 0.23528192169001277 chrY 59373566 158935 0.002676864650507938 0.07468955658835474