BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504713.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,077,317 number of mapped reads = 1,879,426 (90.47%) number of secondary alignments = 0 number of mapped bases = 60,135,678 bp number of sequenced bases = 60,135,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,776 duplication rate = 7.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.8559 >>>>>>> ACTG content number of A's = 17,445,522 bp (29.01%) number of C's = 12,006,323 bp (19.97%) number of T's = 18,525,598 bp (30.81%) number of G's = 12,158,160 bp (20.22%) number of N's = 75 bp (0%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 30,179 >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.5642X There is a 1.04% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 4910538 0.01970120668224935 0.37690088334806043 chr2 243199373 5281918 0.0217184688218748 0.6096802234612296 chr3 198022430 4304498 0.021737426411745378 0.366093443968952 chr4 191154276 4212956 0.022039559292934677 0.2834595397242261 chr5 180915260 3757404 0.020768861620628354 0.34784918031075385 chr6 171115067 3926000 0.022943625414353488 0.3785657979490014 chr7 159138663 5836662 0.0366765805993984 1.9012160834890612 chr8 146364022 3386606 0.02313824089911932 0.4369934567312332 chr9 141213431 2588892 0.0183331853186118 0.4016612679778699 chr10 135534747 2808720 0.020723246711044512 0.36393521586630834 chr11 135006516 2817348 0.020868237204195388 0.34651099644110545 chr12 133851895 3228962 0.024123393994534035 0.5254864242470458 chr13 115169878 2119710 0.018405072895883418 0.4447612996511361 chr14 107349540 1622472 0.01511391665022505 0.21258365583474062 chr15 102531392 1150802 0.011223899115697171 0.16399712147552759 chr16 90354753 1726444 0.019107395490306968 0.4436840599710946 chr17 81195210 1093554 0.013468208284700538 0.31481851303200786 chr18 78077248 1468988 0.01881454633237073 0.2757136524930982 chr19 59128983 672438 0.01137239245261499 0.16944433069530496 chr20 63025520 813274 0.012903884013967675 0.18289306294770966 chr21 48129895 515436 0.010709269155895727 0.18902957361553824 chr22 51304566 353754 0.006895175762718663 0.11810220545065177 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 794172 0.005114762257571558 0.08371794914903063 chrY 59373566 744098 0.012532479521273827 0.27497613399155396