BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089401.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 = 21,962,820 number of mapped reads = 20,254,887 (92.22%) number of supplementary alignments = 93,860 (0.43%) number of secondary alignments = 0 number of mapped bases = 1,334,497,163 bp number of sequenced bases = 1,334,031,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,909,111 duplication rate = 12.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8698 >>>>>>> ACTG content number of A's = 346,915,781 bp (26.01%) number of C's = 258,137,138 bp (19.35%) number of T's = 407,159,694 bp (30.52%) number of G's = 321,093,359 bp (24.07%) number of N's = 725,551 bp (0.05%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 10,113,571 number of insertions = 90,181 mapped reads with insertion percentage = 0.44% number of deletions = 260,582 mapped reads with deletion percentage = 1.27% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.4311X std coverageData = 2.7955X There is a 15.96% of reference with a coverageData >= 1X There is a 8.81% of reference with a coverageData >= 2X There is a 5.38% of reference with a coverageData >= 3X There is a 3.46% of reference with a coverageData >= 4X There is a 2.31% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.12% of reference with a coverageData >= 7X There is a 0.81% of reference with a coverageData >= 8X There is a 0.6% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 110767283 0.44440123180274843 4.451541135583948 chr2 243199373 132127715 0.5432897024779747 3.716118031270924 chr3 198022430 82383769 0.416032512074516 1.475829878999356 chr4 191154276 68539603 0.35855647299252674 2.332668764343392 chr5 180915260 68717021 0.3798298772585574 1.3961694542976633 chr6 171115067 83789292 0.4896663600055745 1.9531064281280632 chr7 159138663 65321712 0.4104704084387086 3.4718453277630514 chr8 146364022 70576530 0.4821986239213896 2.5478366411731703 chr9 141213431 73091411 0.5175953199522502 3.0313008545315516 chr10 135534747 49243452 0.3633271400137708 4.217983944703933 chr11 135006516 64478671 0.47759673318286355 3.0086152593430087 chr12 133851895 68131100 0.5090036267323671 1.7000548164336404 chr13 115169878 34027693 0.29545653421635126 1.22180537481414 chr14 107349540 27662238 0.25768380563158444 1.440112822578168 chr15 102531392 38742239 0.3778573395355834 1.3960065652225953 chr16 90354753 35670132 0.39477870079507604 1.898160994526963 chr17 81195210 32325378 0.3981192732921068 1.8764802568371897 chr18 78077248 35939501 0.46030696420037753 4.619979305339123 chr19 59128983 29553924 0.4998212805385136 3.2198326080056217 chr20 63025520 30444400 0.48304877135484164 1.8665004146499564 chr21 48129895 15537359 0.32282137744119327 2.2427612554694134 chr22 51304566 21919366 0.42724006280454646 1.580359799803242 chrMT 16571 104520 6.307404501840565 7.056003542953305 chrX 155270560 91388003 0.5885726373370458 2.330691218237206 chrY 59373566 4014851 0.06762017629192088 2.191990521335173