BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063567.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 = 1,662,000 number of mapped reads = 1,497,112 (90.08%) number of supplementary alignments = 10,161 (0.61%) number of secondary alignments = 0 number of mapped bases = 99,897,319 bp number of sequenced bases = 99,850,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,767 duplication rate = 2.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7333 >>>>>>> ACTG content number of A's = 28,186,518 bp (28.23%) number of C's = 18,373,734 bp (18.4%) number of T's = 31,341,975 bp (31.39%) number of G's = 21,946,371 bp (21.98%) number of N's = 2,168 bp (0%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 807,729 number of insertions = 7,921 mapped reads with insertion percentage = 0.52% number of deletions = 28,332 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.3195X There is a 2.88% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 10166806 0.04078949115236106 0.6109594609508399 chr2 243199373 9996196 0.04110288557364003 0.39454616463035075 chr3 198022430 6825489 0.034468262004460806 0.20254379274681672 chr4 191154276 5210734 0.027259311740428973 0.18247741321171843 chr5 180915260 4543968 0.025116554568144225 0.1722919315682349 chr6 171115067 7259337 0.04242371596651977 0.2545718872534707 chr7 159138663 6906591 0.04339983049876447 0.46943578780179257 chr8 146364022 3701680 0.025290914730397338 0.4116654366607004 chr9 141213431 3167172 0.022428263215274472 0.26493461253207934 chr10 135534747 4635682 0.034202904440438435 0.28169596569012356 chr11 135006516 5598856 0.04147100574019701 0.2649361392873385 chr12 133851895 3624008 0.02707476050301716 0.18537479501374354 chr13 115169878 2604482 0.022614263774769303 0.16265236379920842 chr14 107349540 1869679 0.0174167397456943 0.16138469739672437 chr15 102531392 1676432 0.01635042660885751 0.14225776145039243 chr16 90354753 2059583 0.022794406842106027 0.18268215431021687 chr17 81195210 3039452 0.037433883107143885 0.22896896433474603 chr18 78077248 3257392 0.04172011800415916 0.4599080892897879 chr19 59128983 2056519 0.03478021937228313 0.4300525070537829 chr20 63025520 1449325 0.02299584358843846 0.17021729059583465 chr21 48129895 1733322 0.03601341744044943 0.21345535406120075 chr22 51304566 965579 0.01882052759202758 0.14731270850894132 chrMT 16571 3650 0.22026431718061673 0.504283458889049 chrX 155270560 7329581 0.04720522035857924 0.2638922262701794 chrY 59373566 215804 0.0036346814675069375 0.09917345229211762