BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080713.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 = 1,858,384 number of mapped reads = 1,691,830 (91.04%) number of supplementary alignments = 11,902 (0.64%) number of secondary alignments = 0 number of mapped bases = 114,930,425 bp number of sequenced bases = 114,888,099 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,505 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4269 >>>>>>> ACTG content number of A's = 32,287,330 bp (28.1%) number of C's = 21,199,776 bp (18.45%) number of T's = 36,626,044 bp (31.88%) number of G's = 24,773,115 bp (21.56%) number of N's = 1,834 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 871,400 number of insertions = 7,928 mapped reads with insertion percentage = 0.47% number of deletions = 23,965 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.0371X std coverageData = 0.3147X There is a 3.09% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 13764104 0.05522194466267749 0.45140015070957945 chr2 243199373 7487567 0.030787772631305263 0.29466782298170596 chr3 198022430 7234735 0.03653492687671796 0.22071705610673026 chr4 191154276 4901912 0.025643747566494405 0.1886049468681866 chr5 180915260 5413119 0.029920743004210923 0.1990913269509529 chr6 171115067 7012764 0.04098273824127948 0.28361738727566044 chr7 159138663 7296136 0.04584766431021228 0.7398202778179095 chr8 146364022 13878009 0.0948184452050655 0.4499484783970397 chr9 141213431 3517449 0.024908742568545056 0.21006622874573283 chr10 135534747 5501296 0.04058956187818021 0.2885643833922291 chr11 135006516 4754474 0.03521662613677106 0.22742412495650233 chr12 133851895 3728485 0.027855302310064417 0.19368719068214213 chr13 115169878 2412732 0.020949331907775398 0.16680104113215238 chr14 107349540 2246105 0.020923284813330358 0.17281787084009004 chr15 102531392 2160424 0.021070854085351733 0.16663893847069533 chr16 90354753 2693872 0.029814391723255555 0.20674854809851384 chr17 81195210 1870568 0.02303791073389674 0.1808217563542322 chr18 78077248 3598769 0.046092416064664576 0.3479024230036319 chr19 59128983 1927066 0.032590886942871995 0.3123837584016722 chr20 63025520 2683408 0.042576530903672034 0.2428780936715652 chr21 48129895 1730582 0.035956488166034854 0.22503063860798786 chr22 51304566 1101281 0.021465555326985904 0.1679781043048457 chrMT 16571 16696 1.0075432985335828 1.254286166390877 chrX 155270560 7751945 0.049925401183585606 0.2671786499506413 chrY 59373566 246927 0.004158870969616344 0.08830397095412072