BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236124.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 = 2,147,735 number of mapped reads = 1,811,419 (84.34%) number of supplementary alignments = 12,553 (0.58%) number of secondary alignments = 0 number of mapped bases = 119,206,392 bp number of sequenced bases = 119,146,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,330 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1549 >>>>>>> ACTG content number of A's = 32,583,552 bp (27.35%) number of C's = 21,308,580 bp (17.88%) number of T's = 38,634,644 bp (32.43%) number of G's = 26,571,301 bp (22.3%) number of N's = 48,251 bp (0.04%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 951,044 number of insertions = 8,316 mapped reads with insertion percentage = 0.45% number of deletions = 34,232 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.3904X There is a 3.04% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10549014 0.042322919628753904 0.7490846158398953 chr2 243199373 5534518 0.022757122815444102 0.3386509105694659 chr3 198022430 4314419 0.021787526796838114 0.17848427044388607 chr4 191154276 7859083 0.041113822638212914 0.25323916306253785 chr5 180915260 4429156 0.02448193701294186 0.19188840106605384 chr6 171115067 13114436 0.07664103594103727 0.42180425233143987 chr7 159138663 8919931 0.05605131293581372 0.6324727038096827 chr8 146364022 8770889 0.059925170681631036 0.6534779322355964 chr9 141213431 4064059 0.028779550013199522 0.2569038058835171 chr10 135534747 6788393 0.05008599750438904 0.326267633477798 chr11 135006516 6840057 0.050664643475430475 0.33498464164835 chr12 133851895 3621294 0.027054484361241207 0.20153407071497176 chr13 115169878 5222310 0.04534440854404656 0.2604570203167443 chr14 107349540 2731163 0.025441776462200024 0.19930922886545724 chr15 102531392 1994703 0.019454558853546043 0.1731047791046583 chr16 90354753 3488572 0.03860972316531041 0.2456785597748333 chr17 81195210 4064607 0.050059689481682476 0.3387065938416682 chr18 78077248 2118687 0.027135779683218342 0.3553164299205781 chr19 59128983 2589511 0.04379427598137448 0.5267647812728953 chr20 63025520 2102638 0.03336169221610548 0.2235308024153611 chr21 48129895 1697274 0.035264444271071026 0.23195132494196685 chr22 51304566 1368845 0.026680763657566074 0.1943861121691838 chrMT 16571 154568 9.327620541910566 5.948740511955828 chrX 155270560 6609451 0.042567316044973366 0.264026074956927 chrY 59373566 258814 0.0043590779101932335 0.09717952268431605