BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,380,906 number of mapped reads = 8,980,035 (86.51%) number of secondary alignments = 0 number of mapped bases = 356,542,802 bp number of sequenced bases = 356,503,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 789,094 duplication rate = 7.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6893 >>>>>>> ACTG content number of A's = 107,973,334 bp (30.29%) number of C's = 69,766,771 bp (19.57%) number of T's = 108,428,300 bp (30.41%) number of G's = 70,331,608 bp (19.73%) number of N's = 3,630 bp (0%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 1,026,682 number of insertions = 10,705 mapped reads with insertion percentage = 0.12% number of deletions = 30,276 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.1152X std coverageData = 0.9579X There is a 8.61% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 28423282 0.11403494958594305 1.5227517991226507 chr2 243199373 31412928 0.12916533300437416 0.6313303008569053 chr3 198022430 25335971 0.1279449555285227 0.45035722981867715 chr4 191154276 25438703 0.1330794347493435 0.496168447299213 chr5 180915260 23398516 0.12933412029477226 0.461297724920826 chr6 171115067 22086755 0.12907545423805375 0.5528069645137536 chr7 159138663 19836712 0.1246504879835518 0.9329472494357062 chr8 146364022 19106535 0.13054119953057863 2.947057534737337 chr9 141213431 15160747 0.10736051728677282 0.5996509374865904 chr10 135534747 16751723 0.12359725731439186 0.6948826700791373 chr11 135006516 16608714 0.12302157326984128 0.6072601159061868 chr12 133851895 16435600 0.12278944575271049 0.4630614155674546 chr13 115169878 12701337 0.11028349791253578 0.4138948441395769 chr14 107349540 11101560 0.10341506819684555 0.48092538039322524 chr15 102531392 9827610 0.09584976667438593 0.3837816610421121 chr16 90354753 8969453 0.09926929909265537 0.45049343594833824 chr17 81195210 8200932 0.10100265766909157 0.44918094729559116 chr18 78077248 10023311 0.12837684801595467 1.271397476548693 chr19 59128983 5555049 0.09394798824799676 1.1330893263640536 chr20 63025520 6955210 0.11035545601210431 0.4518842806256614 chr21 48129895 4685638 0.09735400420050781 0.4757469513039745 chr22 51304566 3272687 0.06378939059732032 0.35224954304587536 chrMT 16571 5615 0.3388449701285378 0.747039330495005 chrX 155270560 12069774 0.0777338215306237 0.48514567690046495 chrY 59373566 3178440 0.0535329139570293 0.5693330004504475