BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080762.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,801,876 number of mapped reads = 5,056,439 (74.34%) number of supplementary alignments = 29,326 (0.43%) number of secondary alignments = 0 number of mapped bases = 325,212,293 bp number of sequenced bases = 325,098,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 703,408 duplication rate = 10.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1612 >>>>>>> ACTG content number of A's = 100,791,560 bp (31%) number of C's = 65,142,617 bp (20.04%) number of T's = 84,806,942 bp (26.09%) number of G's = 74,253,129 bp (22.84%) number of N's = 104,641 bp (0.03%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,575,012 number of insertions = 22,847 mapped reads with insertion percentage = 0.45% number of deletions = 61,520 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.1051X std coverageData = 0.6758X There is a 6.43% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% 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% 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 40806018 0.16371480976169764 1.0173643456775046 chr2 243199373 25296549 0.10401568346148655 0.6427721181524552 chr3 198022430 19708710 0.09952766461859902 0.48546700795957326 chr4 191154276 19254389 0.10072695941156974 0.5558695764078279 chr5 180915260 17589113 0.09722293741279757 0.48207455250007886 chr6 171115067 21777598 0.12726873431899483 0.7697295915554789 chr7 159138663 22254685 0.13984461463019832 1.0327089571130097 chr8 146364022 15117598 0.1032876645054206 0.9175469978523584 chr9 141213431 11522928 0.08159937704509142 0.5307430777734446 chr10 135534747 14299391 0.10550350604926426 0.6896635814036203 chr11 135006516 13150894 0.09740932800606454 0.638268225465553 chr12 133851895 12842079 0.09594245191672482 0.4833179456145842 chr13 115169878 13114629 0.11387204039584031 0.5279896574462443 chr14 107349540 8986626 0.08371368894547662 0.5015590237991752 chr15 102531392 8481971 0.08272560076039931 0.44644275973592773 chr16 90354753 9620279 0.10647230699640117 0.5440502606155654 chr17 81195210 7462460 0.09190763839393974 0.4903079042136595 chr18 78077248 4705551 0.06026789007727321 0.7424100901942017 chr19 59128983 5998376 0.10144561424301853 0.932122968866124 chr20 63025520 6577226 0.10435813936957601 0.5203800825980286 chr21 48129895 5166935 0.10735396368514828 0.5933667436629008 chr22 51304566 3480027 0.06783074629263992 0.40946599381307464 chrMT 16571 158343 9.555428157624766 8.043029615196188 chrX 155270560 16927485 0.10901928221293206 0.5385541991977264 chrY 59373566 912433 0.015367663784924086 0.4184428478245824