BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240059.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 = 1,414,805 number of mapped reads = 1,075,076 (75.99%) number of supplementary alignments = 9,524 (0.67%) number of secondary alignments = 0 number of mapped bases = 71,572,526 bp number of sequenced bases = 71,534,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,097 duplication rate = 8.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0237 >>>>>>> ACTG content number of A's = 20,154,360 bp (28.17%) number of C's = 13,169,601 bp (18.41%) number of T's = 22,983,137 bp (32.13%) number of G's = 15,221,118 bp (21.28%) number of N's = 6,699 bp (0.01%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 610,048 number of insertions = 5,150 mapped reads with insertion percentage = 0.48% number of deletions = 21,487 mapped reads with deletion percentage = 1.97% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.29X There is a 1.28% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 5727569 0.022979156388942358 0.4123206838370631 chr2 243199373 7739120 0.03182212151509124 0.33357215639717513 chr3 198022430 4529787 0.022875120762834798 0.24489529786948935 chr4 191154276 4739213 0.024792607830546255 0.2603930073053762 chr5 180915260 3845789 0.021257405262552202 0.23455981603501416 chr6 171115067 3707570 0.02166711596472098 0.25396106440951155 chr7 159138663 4248703 0.026698119237058063 0.3510533564481936 chr8 146364022 4066875 0.027786029274325354 0.3788768503940228 chr9 141213431 2606613 0.01845867621472918 0.2515994204733674 chr10 135534747 3526711 0.02602071482082746 0.2965146908465321 chr11 135006516 3115725 0.023078330530357512 0.2782007180070191 chr12 133851895 3326119 0.02484924849214873 0.25725968454255765 chr13 115169878 1869411 0.016231770255066173 0.20728421371385752 chr14 107349540 2328720 0.021692873579150874 0.2427073625960726 chr15 102531392 2031814 0.019816506538797407 0.22835377261919074 chr16 90354753 2079788 0.023018025404817385 0.24347585508887126 chr17 81195210 1728583 0.02128922383475577 0.25818453999212665 chr18 78077248 1680069 0.021518035574204664 0.38291940865926954 chr19 59128983 1242460 0.02101270708478108 0.2972188665281648 chr20 63025520 1448941 0.022989750818398644 0.24710910774555642 chr21 48129895 1125483 0.023384281224798017 0.2518162260854567 chr22 51304566 616656 0.012019514988198126 0.16740669951135545 chrMT 16571 8664 0.5228411079596886 1.0186356832137455 chrX 155270560 4025849 0.0259279608446057 0.2712572852460277 chrY 59373566 206294 0.0034745091780406115 0.08870630233474054