BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716531.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 = 1,731,887 number of mapped reads = 1,578,121 (91.12%) number of supplementary alignments = 28,686 (1.66%) number of secondary alignments = 0 number of mapped bases = 125,853,810 bp number of sequenced bases = 125,795,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,118 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7442 >>>>>>> ACTG content number of A's = 33,745,081 bp (26.83%) number of C's = 24,657,354 bp (19.6%) number of T's = 37,197,416 bp (29.57%) number of G's = 30,186,522 bp (24%) number of N's = 8,840 bp (0.01%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 818,725 number of insertions = 11,590 mapped reads with insertion percentage = 0.72% number of deletions = 30,723 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3642X There is a 3.51% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12331501 0.04947430401788247 0.7233492471127259 chr2 243199373 10340658 0.04251926258050016 0.3998619032594691 chr3 198022430 8034340 0.040572878537042494 0.22220108342602482 chr4 191154276 7834403 0.0409847122645585 0.2754114709311395 chr5 180915260 7222897 0.03992419987125464 0.2237405134936646 chr6 171115067 6907642 0.04036840309334069 0.24111181383864394 chr7 159138663 6612172 0.041549752117749035 0.426239834004093 chr8 146364022 6182942 0.04224359180290905 0.40947320740607795 chr9 141213431 5129958 0.03632769180432986 0.306801799081719 chr10 135534747 5766924 0.042549413546328456 0.35452479851687174 chr11 135006516 6942308 0.05142202173412134 0.41950719319077917 chr12 133851895 5468407 0.04085416198254048 0.22591168644476872 chr13 115169878 4400214 0.038206292100092354 0.2205098408247849 chr14 107349540 3663416 0.03412605214703295 0.21742783414677064 chr15 102531392 3538962 0.03451588758299507 0.2060403590849699 chr16 90354753 2852170 0.031566352685397744 0.21997778493206066 chr17 81195210 3894138 0.04796019371093443 0.2913610044932875 chr18 78077248 3244946 0.04156071177098865 0.5148473830789064 chr19 59128983 2433003 0.04114738452376223 0.47912026465400087 chr20 63025520 2634718 0.04180398670252939 0.23832998168699004 chr21 48129895 1630649 0.033880169487176315 0.2367095610189179 chr22 51304566 1490430 0.029050630698250132 0.19089421151922012 chrMT 16571 113274 6.835676784744433 4.451286204754962 chrX 155270560 6819149 0.043917848947025113 0.27182144684767173 chrY 59373566 364589 0.0061405946208452425 0.19447997316190282