BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054578.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,868,221 number of mapped reads = 7,040,646 (71.35%) number of supplementary alignments = 213 (0%) number of secondary alignments = 0 number of mapped bases = 333,177,453 bp number of sequenced bases = 333,106,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,041,368 duplication rate = 21.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4639 >>>>>>> ACTG content number of A's = 97,375,635 bp (29.23%) number of C's = 64,347,990 bp (19.32%) number of T's = 99,687,612 bp (29.93%) number of G's = 71,575,942 bp (21.49%) number of N's = 119,807 bp (0.04%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,880,824 number of insertions = 13,560 mapped reads with insertion percentage = 0.19% number of deletions = 47,330 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.1076X std coverageData = 0.8848X There is a 4.14% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 29624083 0.11885259455381658 0.994120137489538 chr2 243199373 34993994 0.14389014892731652 1.1438570591375343 chr3 198022430 22725676 0.11476314072097792 0.8554629895568384 chr4 191154276 16149293 0.08448303296129248 0.7231387303575936 chr5 180915260 19025423 0.10516206869448161 0.8297025008201746 chr6 171115067 20270143 0.11845913603855819 0.916735944292321 chr7 159138663 17224237 0.10823414420667843 0.9061011825659332 chr8 146364022 18124552 0.12383201658669915 0.9360424593159087 chr9 141213431 17204295 0.12183186031362697 0.9089411986865723 chr10 135534747 11457912 0.08453855748149956 0.7850556532315032 chr11 135006516 13865036 0.10269901343132208 0.8544771649091791 chr12 133851895 17551328 0.13112498706125902 0.9334072853269085 chr13 115169878 9150003 0.07944788306539667 0.7168372464677674 chr14 107349540 6377343 0.059407269001804756 0.6628529494307029 chr15 102531392 8342121 0.08136162825137495 0.6908320126426976 chr16 90354753 8094483 0.08958558051727505 0.8148154299844247 chr17 81195210 7661923 0.0943642241949987 0.7478156068550222 chr18 78077248 10357813 0.13266109225571066 1.0485703245029567 chr19 59128983 6834336 0.11558352018332532 0.9754971992004737 chr20 63025520 7152631 0.11348785380906021 0.8888121746459127 chr21 48129895 3799822 0.07894930998706728 0.7525456215256806 chr22 51304566 4699533 0.09160067741339045 0.767274734680166 chrMT 16571 22922 1.3832599118942732 3.224363034245482 chrX 155270560 21657333 0.13948125774776624 0.997580466302373 chrY 59373566 811218 0.013662948929158137 0.2840141481402604