BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818820.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,109,803 number of mapped reads = 1,081,351 (97.44%) number of supplementary alignments = 7,532 (0.68%) number of secondary alignments = 0 number of mapped bases = 73,431,789 bp number of sequenced bases = 73,401,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,115 duplication rate = 29.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6669 >>>>>>> ACTG content number of A's = 19,955,318 bp (27.19%) number of C's = 15,184,620 bp (20.69%) number of T's = 21,573,124 bp (29.39%) number of G's = 16,684,330 bp (22.73%) number of N's = 4,219 bp (0.01%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 369,822 number of insertions = 8,513 mapped reads with insertion percentage = 0.77% number of deletions = 18,398 mapped reads with deletion percentage = 1.68% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.3461X There is a 1.34% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 6100445 0.02447514463765368 0.46254917303963194 chr2 243199373 6485034 0.02666550460226721 0.6132479884205149 chr3 198022430 4978011 0.02513862192277915 0.2582264247081288 chr4 191154276 4611114 0.024122473723789468 0.28408485043991827 chr5 180915260 4551101 0.025155981866869605 0.27140035295524156 chr6 171115067 4327182 0.02528814134175572 0.2790893969489781 chr7 159138663 4021177 0.025268384968145673 0.29544708213828313 chr8 146364022 3741054 0.025559928928435706 0.2774772389012838 chr9 141213431 3164839 0.022411742123877722 0.2842073808986193 chr10 135534747 3560394 0.026269234117506413 0.3541019866626786 chr11 135006516 3534699 0.02618169185256214 0.2911269021477611 chr12 133851895 3371213 0.02518614323689627 0.2711860676807184 chr13 115169878 2311647 0.020071628451321273 0.2297780142378927 chr14 107349540 2206360 0.02055304568608305 0.257931776261602 chr15 102531392 2113629 0.02061445727763064 0.24017376439760732 chr16 90354753 2291199 0.025357813772121096 0.41150420771035395 chr17 81195210 2042072 0.02515015356201431 0.2806773978605417 chr18 78077248 2024112 0.025924479305418142 0.3410179745762278 chr19 59128983 1540301 0.02604984766945848 0.39249434250532206 chr20 63025520 1590620 0.025237713231084806 0.27277016075781574 chr21 48129895 1017039 0.02113112858442762 0.2590046402219243 chr22 51304566 939601 0.01831417889783923 0.2428301307600787 chrMT 16571 55822 3.368656085933257 4.831475719335903 chrX 155270560 2187459 0.014088047341363359 0.20670468904583666 chrY 59373566 665665 0.011211470774721531 0.5609552926545719