BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238537.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 = 5,973,832 number of mapped reads = 5,434,723 (90.98%) number of supplementary alignments = 40,570 (0.68%) number of secondary alignments = 0 number of mapped bases = 338,314,425 bp number of sequenced bases = 338,147,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,757,778 duplication rate = 20.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3117 >>>>>>> ACTG content number of A's = 84,017,015 bp (24.85%) number of C's = 60,351,061 bp (17.85%) number of T's = 112,638,732 bp (33.31%) number of G's = 81,116,498 bp (23.99%) number of N's = 23,874 bp (0.01%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,907,111 number of insertions = 21,482 mapped reads with insertion percentage = 0.39% number of deletions = 98,653 mapped reads with deletion percentage = 1.8% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.1093X std coverageData = 1.4648X There is a 4.07% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 0.94% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 42989852 0.17247640879498552 2.1085590108788015 chr2 243199373 33433522 0.13747371791127108 3.491897597239099 chr3 198022430 21331263 0.1077214485247959 0.7747512074751687 chr4 191154276 25119447 0.13140928639231697 0.8118156099242275 chr5 180915260 24005124 0.13268711550368942 0.8300658364230412 chr6 171115067 16452096 0.09614639019485058 1.3390066531577645 chr7 159138663 15783170 0.09917872691942875 1.1956058224685735 chr8 146364022 23331799 0.15940938682321806 1.0769377221141851 chr9 141213431 7599695 0.05381708344725368 0.6162115302376434 chr10 135534747 19789675 0.14601181938975397 1.3021132280728125 chr11 135006516 8195571 0.0607050033051738 0.5867030230181817 chr12 133851895 7652307 0.05716995639097975 0.5361610230223302 chr13 115169878 9660761 0.0838827058582106 0.9432916650538075 chr14 107349540 9633348 0.0897381395393031 0.6848376258628457 chr15 102531392 4414697 0.04305702784177552 0.7769480919410631 chr16 90354753 7951132 0.08799904527435319 0.7417442444858752 chr17 81195210 7350617 0.090530180290192 0.676863950069341 chr18 78077248 11028145 0.1412465895314343 2.489596586218348 chr19 59128983 5329276 0.09012967464703392 1.4685767806940306 chr20 63025520 8268108 0.13118666851142205 0.8384800338729211 chr21 48129895 3856833 0.08013383365993215 0.6558779339980926 chr22 51304566 3117010 0.06075502129771451 0.5580929637194949 chrMT 16571 59252 3.575644197694768 4.267011789028317 chrX 155270560 21069443 0.13569502808516953 0.846522485848803 chrY 59373566 892282 0.015028270324878246 0.5302459567243348