BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063561.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,963,797 number of mapped reads = 1,495,796 (76.17%) number of supplementary alignments = 15,935 (0.81%) number of secondary alignments = 0 number of mapped bases = 94,313,068 bp number of sequenced bases = 94,276,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,403 duplication rate = 12.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2012 >>>>>>> ACTG content number of A's = 25,426,835 bp (26.97%) number of C's = 17,074,184 bp (18.11%) number of T's = 30,274,000 bp (32.11%) number of G's = 21,499,925 bp (22.81%) number of N's = 1,764 bp (0%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 748,576 number of insertions = 7,548 mapped reads with insertion percentage = 0.5% number of deletions = 22,718 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.3871X There is a 1.44% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% 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% 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 8385257 0.03364187004372599 0.5066351708375677 chr2 243199373 7726938 0.031772030925425125 0.5564541812346603 chr3 198022430 5541445 0.027983925861327932 0.31173007316501 chr4 191154276 5453931 0.02853156682720506 0.32608462629385077 chr5 180915260 6046761 0.033423167288375785 0.3432113354232859 chr6 171115067 5120478 0.029924179616515008 0.3563934372456987 chr7 159138663 5657758 0.03555237861964443 0.4355828297687765 chr8 146364022 4942504 0.033768571896719266 0.434865240581338 chr9 141213431 3551215 0.02514785580133663 0.3303433140967318 chr10 135534747 4582311 0.033809123501001556 0.3887589097836419 chr11 135006516 4058676 0.03006281563476536 0.34940892616871644 chr12 133851895 4349732 0.032496603802284606 0.3356552044894124 chr13 115169878 2655525 0.02305746125736106 0.2903719576341314 chr14 107349540 2766456 0.025770543590592006 0.32899726810692487 chr15 102531392 2705609 0.026388103655122522 0.329993505983416 chr16 90354753 2813514 0.03113852793112057 0.3319857038074772 chr17 81195210 2361164 0.029080089823032663 0.3119223903659376 chr18 78077248 2519145 0.032264777057715965 0.45957276476589864 chr19 59128983 2055676 0.03476596240459607 0.4028051277283977 chr20 63025520 2100692 0.0333308158346016 0.34236846225268036 chr21 48129895 1302309 0.027058214026853787 0.3049048639631136 chr22 51304566 1082235 0.021094321312453944 0.2639031829253154 chrMT 16571 28576 1.7244583911652887 2.1735357368795407 chrX 155270560 6217354 0.040042065926728154 0.3881439482513 chrY 59373566 287807 0.004847392861665072 0.1366357364992549