BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046491.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 13,214,848 number of mapped reads = 13,165,972 (99.63%) number of supplementary alignments = 50,358 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,596,484 number of mapped paired reads (second in pair) = 6,569,488 number of mapped paired reads (both in pair) = 13,129,780 number of mapped paired reads (singletons) = 36,192 number of mapped bases = 1,298,707,936 bp number of sequenced bases = 1,298,389,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,520,709 duplication rate = 35.01% >>>>>>> Insert size mean insert size = 15,192.8773 std insert size = 1,223,915.5932 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.9084 >>>>>>> ACTG content number of A's = 372,186,121 bp (28.67%) number of C's = 275,837,845 bp (21.24%) number of T's = 374,530,700 bp (28.85%) number of G's = 275,712,210 bp (21.23%) number of N's = 122,855 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 4,569,478 number of insertions = 94,311 mapped reads with insertion percentage = 0.7% number of deletions = 118,902 mapped reads with deletion percentage = 0.88% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.4195X std coverageData = 26.5857X There is a 4.83% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192216433 0.7711773484407889 36.96689878985689 chr2 243199373 132673782 0.5455350495496549 27.78827340567145 chr3 198022430 69361700 0.3502719363659965 24.03627650190809 chr4 191154276 26301752 0.13759436906344696 9.864789531871399 chr5 180915260 65918885 0.3643633212588037 21.288753772667263 chr6 171115067 104962171 0.6134011039483741 39.368409814859305 chr7 159138663 92942388 0.5840339880196178 27.332700409133594 chr8 146364022 177525081 1.2129010843935404 54.86365726548648 chr9 141213431 31182225 0.2208162834029576 17.657913310386494 chr10 135534747 47340804 0.3492890572186629 22.901738331460606 chr11 135006516 43979735 0.32576009146106694 22.203369528210267 chr12 133851895 35736788 0.26698753872703856 16.20572237650202 chr13 115169878 31150089 0.2704707996651694 19.015455788890826 chr14 107349540 34978427 0.32583676651059706 21.31226914017491 chr15 102531392 11141229 0.10866163798888052 4.222957291780738 chr16 90354753 70562535 0.7809498964597911 41.011952477498355 chr17 81195210 24796504 0.30539368024296015 13.093920506188425 chr18 78077248 12419605 0.15906817053797798 6.900590552782894 chr19 59128983 8256665 0.13963820416123174 6.091453105796451 chr20 63025520 16904762 0.26822090480173744 12.26099200106393 chr21 48129895 12050721 0.25037912507392757 24.91725740490896 chr22 51304566 4328237 0.08436358276571329 4.211525780420276 chrMT 16571 97051 5.856677327861927 3.303489516940108 chrX 155270560 51644619 0.3326105025962423 25.20020990609847 chrY 59373566 235748 0.003970588527561238 0.5157890926236275