BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472482.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 301,816 number of mapped reads = 297,720 (98.64%) number of supplementary alignments = 1,128 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 149,501 number of mapped paired reads (second in pair) = 148,219 number of mapped paired reads (both in pair) = 295,626 number of mapped paired reads (singletons) = 2,094 number of mapped bases = 29,313,791 bp number of sequenced bases = 29,310,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,323 duplication rate = 17.26% >>>>>>> Insert size mean insert size = 27,140.0447 std insert size = 1,567,337.2045 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.1004 >>>>>>> ACTG content number of A's = 8,139,929 bp (27.77%) number of C's = 6,555,159 bp (22.36%) number of T's = 8,104,350 bp (27.65%) number of G's = 6,506,276 bp (22.2%) number of N's = 4,534 bp (0.02%) GC percentage = 44.56% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 183,812 number of insertions = 1,672 mapped reads with insertion percentage = 0.55% number of deletions = 1,497 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.2543X There is a 0.35% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.05% 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 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% 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 3135279 0.01257882121786168 0.3179361391557384 chr2 243199373 2078865 0.008547986675936044 0.2418955599250363 chr3 198022430 3287026 0.0165992610029076 0.3096396918398275 chr4 191154276 1099676 0.0057528192568394336 0.18411053515700415 chr5 180915260 1583759 0.008754148212815215 0.22244505850235727 chr6 171115067 1911751 0.011172312488414594 0.2709684852517876 chr7 159138663 1249363 0.00785078230800519 0.21071880762363446 chr8 146364022 1312515 0.00896747016148545 0.24108486114406225 chr9 141213431 1766168 0.012507082276047807 0.26881656253859143 chr10 135534747 891111 0.006574778938422337 0.2670427003225303 chr11 135006516 1280020 0.009481172005060852 0.2542662961602117 chr12 133851895 1600537 0.01195752215536433 0.31808100954460644 chr13 115169878 618619 0.005371361077590097 0.17075427978728153 chr14 107349540 807808 0.007525025258608467 0.3329974908811912 chr15 102531392 749271 0.007307722887445047 0.21200276360618067 chr16 90354753 959289 0.010616917961139245 0.24359266404183366 chr17 81195210 1070689 0.013186603002812604 0.27100854437138133 chr18 78077248 598622 0.007667047895950431 0.24390474327471573 chr19 59128983 570278 0.009644644150230015 0.24332932874342755 chr20 63025520 646419 0.010256464365545894 0.2702113128000646 chr21 48129895 123964 0.002575613348003356 0.09669824030820354 chr22 51304566 297747 0.005803518540630478 0.17561630131535003 chrMT 16571 432 0.026069639732062035 0.18558548395982333 chrX 155270560 1603676 0.010328268282152135 0.2519747986133374 chrY 59373566 70907 0.0011942520009662213 0.05939433311969539