BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237569.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 = 1,997,286 number of mapped reads = 1,563,092 (78.26%) number of supplementary alignments = 12,882 (0.64%) number of secondary alignments = 0 number of mapped bases = 98,386,868 bp number of sequenced bases = 98,332,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,977 duplication rate = 6.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2744 >>>>>>> ACTG content number of A's = 26,814,513 bp (27.27%) number of C's = 17,048,125 bp (17.34%) number of T's = 32,003,367 bp (32.55%) number of G's = 22,285,788 bp (22.66%) number of N's = 180,642 bp (0.18%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 914,500 number of insertions = 8,213 mapped reads with insertion percentage = 0.52% number of deletions = 33,888 mapped reads with deletion percentage = 2.14% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.3157X There is a 2.45% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7814146 0.03135055779861026 0.5008940263151844 chr2 243199373 8743106 0.0359503640661113 0.36947764080221474 chr3 198022430 7105828 0.03588395516608901 0.2385518418436143 chr4 191154276 6767930 0.035405590403847415 0.24760131205245264 chr5 180915260 6154087 0.03401640635510791 0.2304299180332331 chr6 171115067 5647311 0.03300300259357056 0.2615838448560809 chr7 159138663 5619568 0.03531239922507078 0.3583851654201092 chr8 146364022 4788515 0.03271647591099949 0.4787928754873404 chr9 141213431 4143944 0.029345253993580823 0.30036060069902143 chr10 135534747 4448474 0.03282164978697308 0.32298059944863783 chr11 135006516 4039696 0.029922229827781054 0.27767215225651765 chr12 133851895 4980847 0.037211628569024 0.24496444850836424 chr13 115169878 3320983 0.02883551721744465 0.21304220165482612 chr14 107349540 2923827 0.02723651167950976 0.2229652239839737 chr15 102531392 2890209 0.028188527860813592 0.20969614701852202 chr16 90354753 2179866 0.02412563730875342 0.21033492679034396 chr17 81195210 2324827 0.028632563423384213 0.23288644138270614 chr18 78077248 3046033 0.03901306818600984 0.5215063629707833 chr19 59128983 1722508 0.02913136523927699 0.33842370171106495 chr20 63025520 2011791 0.03192026023744032 0.22845160387908395 chr21 48129895 1338331 0.02780664699143848 0.22124751859949582 chr22 51304566 979315 0.019088262046695805 0.16767880779208919 chrMT 16571 53836 3.248808158831694 2.906832734678958 chrX 155270560 5055660 0.0325603256663723 0.24450397585452485 chrY 59373566 286230 0.004820832220183642 0.12761150758746076