BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524437.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,037,878 number of mapped reads = 2,733,301 (89.97%) number of supplementary alignments = 12,964 (0.43%) number of secondary alignments = 0 number of mapped bases = 159,614,194 bp number of sequenced bases = 159,571,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,430 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6258 >>>>>>> ACTG content number of A's = 39,628,911 bp (24.83%) number of C's = 32,453,361 bp (20.34%) number of T's = 48,843,950 bp (30.61%) number of G's = 38,628,433 bp (24.21%) number of N's = 16,488 bp (0.01%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 807,128 number of insertions = 9,731 mapped reads with insertion percentage = 0.35% number of deletions = 26,000 mapped reads with deletion percentage = 0.94% homopolymer indels = 42.22% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.4898X There is a 4.18% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 13501431 0.054168093727638096 1.0627786783724753 chr2 243199373 12871539 0.0529258724692518 0.6393355173541975 chr3 198022430 10594805 0.053503055184203126 0.2776611270168741 chr4 191154276 10337735 0.05408058462683827 0.39346663030578805 chr5 180915260 9608387 0.05310987586121812 0.27539926794553143 chr6 171115067 6179044 0.03611046127223852 0.2510131501194574 chr7 159138663 9027796 0.05672911805222342 0.6243036966090745 chr8 146364022 8232681 0.05624798285469362 0.36711577045967736 chr9 141213431 5914075 0.04188040017241703 0.3157275947611382 chr10 135534747 8146340 0.060105177309254874 0.5064748304773843 chr11 135006516 6585039 0.04877571242561359 0.35895116528227 chr12 133851895 7517143 0.05616015372811868 0.29372055394717606 chr13 115169878 4966498 0.043123237484023386 0.24762301053261948 chr14 107349540 4416791 0.041144014217480575 0.25515620556648916 chr15 102531392 4972129 0.04849372375633016 0.2644934811934361 chr16 90354753 5160396 0.057112612548451104 0.31298163139062274 chr17 81195210 4596990 0.05661651715661552 0.3225617907161696 chr18 78077248 4279945 0.05481680143234557 0.5982128437919105 chr19 59128983 4925461 0.08330028270569105 0.679348287353691 chr20 63025520 4691124 0.07443213479238252 0.3583895203643253 chr21 48129895 2205573 0.045825427211091986 0.3487781777223215 chr22 51304566 1241721 0.024202933516677638 0.18796477080577795 chrMT 16571 34742 2.0965542212298596 2.1136653131586014 chrX 155270560 9007641 0.05801254919155312 0.32249719753000927 chrY 59373566 599168 0.01009149425183591 0.33869033835969514