BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,343,832 number of mapped reads = 2,740,570 (81.96%) number of supplementary alignments = 12,817 (0.38%) number of secondary alignments = 0 number of mapped bases = 165,760,100 bp number of sequenced bases = 165,708,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,089 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6539 >>>>>>> ACTG content number of A's = 48,153,132 bp (29.06%) number of C's = 33,953,044 bp (20.49%) number of T's = 47,534,635 bp (28.69%) number of G's = 36,065,252 bp (21.76%) number of N's = 1,962 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,236,702 number of insertions = 11,048 mapped reads with insertion percentage = 0.4% number of deletions = 30,411 mapped reads with deletion percentage = 1.1% homopolymer indels = 45.49% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.3571X There is a 4.43% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 13146692 0.05274487159652854 0.5214239593404427 chr2 243199373 14150702 0.05818560231238754 0.4111243785455801 chr3 198022430 12016413 0.0606820803077712 0.2878798609167732 chr4 191154276 10568942 0.05529011550858533 0.2857532669539461 chr5 180915260 9909234 0.054772792521758526 0.2741331406360466 chr6 171115067 9668093 0.056500535981439906 0.3492028563276497 chr7 159138663 8642153 0.054305803737964044 0.47642144446377743 chr8 146364022 8262940 0.0564547208193008 0.4109729211144399 chr9 141213431 6889103 0.048785040850682256 0.3429530514672894 chr10 135534747 8012377 0.05911677394432293 0.3406074913731043 chr11 135006516 7512603 0.05564622525330555 0.3212163354128803 chr12 133851895 7711516 0.05761230350903885 0.28589461620961437 chr13 115169878 5163207 0.044831227484672685 0.24804779699615656 chr14 107349540 4832773 0.04501903780863896 0.2610132639039801 chr15 102531392 4924559 0.04802976828794053 0.2731960434047137 chr16 90354753 4935530 0.05462391115163582 0.29399702011665424 chr17 81195210 4556579 0.05611881538332126 0.3079739389151014 chr18 78077248 4453662 0.05704173897112767 0.5573578645342832 chr19 59128983 3150770 0.053286389180750834 0.4304909560927163 chr20 63025520 3500404 0.05553947036057775 0.28139805058214096 chr21 48129895 2063001 0.04286319344764829 0.25818393648502946 chr22 51304566 1802749 0.03513817853950855 0.21935538790509035 chrMT 16571 89605 5.40733812081347 3.748650983195354 chrX 155270560 9385953 0.060449018796608966 0.32001725439278594 chrY 59373566 410540 0.006914524891430641 0.13703541540875203