BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080788.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 = 2,976,877 number of mapped reads = 2,505,059 (84.15%) number of supplementary alignments = 27,007 (0.91%) number of secondary alignments = 0 number of mapped bases = 160,154,512 bp number of sequenced bases = 160,101,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,618 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1858 >>>>>>> ACTG content number of A's = 46,991,295 bp (29.35%) number of C's = 30,898,898 bp (19.3%) number of T's = 48,637,880 bp (30.38%) number of G's = 33,570,489 bp (20.97%) number of N's = 3,233 bp (0%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,206,905 number of insertions = 11,838 mapped reads with insertion percentage = 0.47% number of deletions = 33,367 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0517X std coverageData = 0.3627X There is a 3.97% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 17315277 0.06946934346855649 0.45517623346813807 chr2 243199373 2371839 0.009752652610662774 0.34324545682253116 chr3 198022430 6995803 0.03532833628998493 0.234725902988326 chr4 191154276 11667212 0.06103557944997265 0.3150351431583046 chr5 180915260 8235597 0.04552184818461417 0.2670869228426702 chr6 171115067 12559003 0.07339507397089702 0.3966295556991178 chr7 159138663 13107757 0.08236689157052927 0.5802729330030033 chr8 146364022 9791876 0.0669008398798989 0.5550480791725535 chr9 141213431 7160382 0.05070609749578282 0.33161990676324093 chr10 135534747 7435773 0.054862484820958866 0.34619233998128424 chr11 135006516 7911388 0.05860004564520427 0.3401521231595602 chr12 133851895 8464316 0.06323643008565549 0.31724790578385575 chr13 115169878 3601236 0.03126890522537499 0.22324995305773457 chr14 107349540 5686748 0.05297412545968991 0.29583762128124486 chr15 102531392 3457882 0.033725105380408765 0.23716146670680438 chr16 90354753 5275441 0.05838587152133546 0.3151077078270975 chr17 81195210 5065385 0.06238526878617593 0.32183242316229715 chr18 78077248 3357592 0.04300346241711798 0.5009908381603749 chr19 59128983 2745803 0.046437514408120294 0.37415779793847315 chr20 63025520 2373744 0.03766321959739483 0.24263161874018108 chr21 48129895 3028091 0.06291497207712587 0.3234505778636157 chr22 51304566 1542423 0.030064049270000646 0.21197105927737783 chrMT 16571 72078 4.349646973628628 3.4222965795619973 chrX 155270560 10566987 0.06805531583063783 0.3405359498283019 chrY 59373566 364879 0.006145478949335804 0.1162160267329251