BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006030.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 = 6,914,010 number of mapped reads = 4,236,384 (61.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,167,639 number of mapped paired reads (second in pair) = 2,068,745 number of mapped paired reads (both in pair) = 3,605,358 number of mapped paired reads (singletons) = 631,026 number of mapped bases = 163,279,260 bp number of sequenced bases = 163,261,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,431 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 74,958.2501 std insert size = 2,641,037.0954 median insert size = 97 >>>>>>> Mapping quality mean mapping quality = 46.354 >>>>>>> ACTG content number of A's = 48,518,917 bp (29.72%) number of C's = 33,424,539 bp (20.47%) number of T's = 47,485,358 bp (29.09%) number of G's = 33,773,106 bp (20.69%) number of N's = 59,443 bp (0.04%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,352,673 number of insertions = 5,207 mapped reads with insertion percentage = 0.12% number of deletions = 14,159 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.3652X There is a 4.24% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12662118 0.050800748055107155 0.480259960570818 chr2 243199373 14446052 0.05940003800914404 0.3368492306683807 chr3 198022430 11763121 0.05940297268344803 0.2902694226252839 chr4 191154276 11030113 0.05770267467100762 0.31098145092767 chr5 180915260 9643044 0.053301440685545265 0.2742571356415848 chr6 171115067 10082997 0.05892524356139837 0.363315822115859 chr7 159138663 8733445 0.05487946697151779 0.3823463860018161 chr8 146364022 8460740 0.05780614583001825 0.7861110311686608 chr9 141213431 6709225 0.04751123850251893 0.2884697232565632 chr10 135534747 7680069 0.05666494511551344 0.4067532402171551 chr11 135006516 7550718 0.05592854496000771 0.3069041190744385 chr12 133851895 7197260 0.053770325776859564 0.2769595602369647 chr13 115169878 5491505 0.047681781863136125 0.259312190608861 chr14 107349540 4850709 0.04518611817060418 0.2630252438071661 chr15 102531392 4527183 0.04415411623398227 0.24932714386949664 chr16 90354753 4434178 0.049075204710038886 0.2983558947654835 chr17 81195210 3917976 0.04825378245834945 0.26763502439583337 chr18 78077248 4471808 0.05727414982659225 0.40899244577291133 chr19 59128983 2772782 0.04689378811064618 0.38973008846014456 chr20 63025520 3296524 0.05230459026756146 0.27941336199550776 chr21 48129895 2235790 0.04645324906692608 0.2765227021101915 chr22 51304566 1567704 0.030556812428741722 0.2141071370478011 chrMT 16571 18900 1.1405467382777141 1.3578957028610097 chrX 155270560 9281980 0.05977939411051264 0.309505373482618 chrY 59373566 453319 0.007635030713836525 0.1822427950346685