BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006211.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,825,538 number of mapped reads = 2,463,825 (87.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,234,277 number of mapped paired reads (second in pair) = 1,229,548 number of mapped paired reads (both in pair) = 2,273,218 number of mapped paired reads (singletons) = 190,607 number of mapped bases = 95,330,284 bp number of sequenced bases = 95,317,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,060 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 60,383.1833 std insert size = 2,313,517.9659 median insert size = 123 >>>>>>> Mapping quality mean mapping quality = 47.7618 >>>>>>> ACTG content number of A's = 26,369,495 bp (27.66%) number of C's = 20,625,196 bp (21.64%) number of T's = 26,939,203 bp (28.26%) number of G's = 21,378,690 bp (22.43%) number of N's = 4,702 bp (0%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 282,513 number of insertions = 3,027 mapped reads with insertion percentage = 0.12% number of deletions = 9,735 mapped reads with deletion percentage = 0.4% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0308X std coverageData = 0.2299X There is a 2.71% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8131040 0.032621944801493594 0.29222205614152474 chr2 243199373 8009063 0.03293208737014301 0.22077864813431947 chr3 198022430 6319935 0.031915248186783686 0.1968675294007442 chr4 191154276 5900900 0.030869829979633834 0.20631792763935383 chr5 180915260 5596991 0.030937086235843233 0.19345656042017215 chr6 171115067 5446136 0.0318273317217589 0.20629774204810952 chr7 159138663 5113825 0.03213439715777931 0.24599647092991894 chr8 146364022 4686489 0.03201940569793853 0.37260330138117775 chr9 141213431 3878199 0.0274633862553768 0.19773761329831527 chr10 135534747 4577875 0.03377639388665402 0.2481713507190345 chr11 135006516 4393837 0.03254536988422099 0.21203689426341837 chr12 133851895 4242424 0.03169491175302374 0.19700992722404395 chr13 115169878 2886718 0.025064869826466257 0.17451982177377376 chr14 107349540 2946803 0.027450541474141388 0.27257361212313896 chr15 102531392 2873947 0.028029922777211492 0.18460796809610125 chr16 90354753 2978909 0.032969034844243336 0.22246827804844044 chr17 81195210 2707944 0.03335103142168116 0.20667553952990525 chr18 78077248 2437206 0.031215316400496084 0.26103781769734014 chr19 59128983 2112182 0.03572160204412783 0.2507623996852977 chr20 63025520 2071083 0.0328610220114011 0.2034698593387916 chr21 48129895 1207861 0.025095857782361668 0.18771792000268092 chr22 51304566 1315632 0.025643565525922195 0.18315798658400786 chrMT 16571 5675 0.3424657534246575 0.6708454396095826 chrX 155270560 5243604 0.03377075473934016 0.2085835310495837 chrY 59373566 246006 0.004143359016030804 0.11488421873697947