BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525016.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 = 6,146,295 number of mapped reads = 5,624,555 (91.51%) number of supplementary alignments = 19,409 (0.32%) number of secondary alignments = 0 number of mapped bases = 325,265,144 bp number of sequenced bases = 325,161,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 476,131 duplication rate = 6.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8057 >>>>>>> ACTG content number of A's = 82,077,537 bp (25.24%) number of C's = 63,207,694 bp (19.44%) number of T's = 102,096,739 bp (31.4%) number of G's = 77,776,037 bp (23.92%) number of N's = 3,223 bp (0%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,620,656 number of insertions = 20,845 mapped reads with insertion percentage = 0.37% number of deletions = 62,998 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.1051X std coverageData = 0.8294X There is a 8.01% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 35530127 0.14254779730318104 1.7668405688069635 chr2 243199373 27753608 0.11411874815976603 0.9955662651426022 chr3 198022430 18143045 0.09162116129975781 0.3896123948881232 chr4 191154276 21207311 0.11094342979803391 0.5274669385403781 chr5 180915260 14304208 0.07906579024898176 0.3819756066350682 chr6 171115067 19193402 0.11216663930593558 0.8418110793212639 chr7 159138663 20974375 0.13179936669444056 1.1358879520189598 chr8 146364022 20593539 0.14070082742055284 0.8072286870894382 chr9 141213431 9332808 0.06609008742235008 0.5887654926514535 chr10 135534747 16628487 0.12268799970534493 0.7955069577143963 chr11 135006516 14224128 0.10535882579178622 0.6882593186833544 chr12 133851895 18275312 0.13653383091812035 0.48287006230395985 chr13 115169878 6483117 0.05629177622294607 0.3147818694012035 chr14 107349540 7582799 0.07063652997488391 0.3582455669469585 chr15 102531392 9182013 0.08955318776906881 0.4209709058810677 chr16 90354753 10720384 0.11864770412243836 0.4861568703165642 chr17 81195210 9445212 0.11632720698671757 0.8013026985334435 chr18 78077248 6518016 0.08348163090994191 1.072266918964791 chr19 59128983 8314242 0.14061195674547625 0.9949130339105742 chr20 63025520 6294222 0.09986783131658414 0.41274169788932374 chr21 48129895 4934034 0.1025149545828014 0.46146100611070173 chr22 51304566 4612736 0.08990887867563288 0.3750629292796031 chrMT 16571 41908 2.528996439563092 2.33657967137641 chrX 155270560 14018275 0.09028289071669478 0.531102404962374 chrY 59373566 957836 0.016132364358913527 0.39054269529791125