BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068083.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 = 3,191,394 number of mapped reads = 2,858,615 (89.57%) number of supplementary alignments = 30,925 (0.97%) number of secondary alignments = 0 number of mapped bases = 191,635,057 bp number of sequenced bases = 191,545,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,854 duplication rate = 5.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1759 >>>>>>> ACTG content number of A's = 54,075,360 bp (28.23%) number of C's = 35,541,576 bp (18.56%) number of T's = 60,625,113 bp (31.65%) number of G's = 41,299,739 bp (21.56%) number of N's = 4,021 bp (0%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,547,657 number of insertions = 15,935 mapped reads with insertion percentage = 0.55% number of deletions = 54,523 mapped reads with deletion percentage = 1.89% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0619X std coverageData = 0.7008X There is a 4.43% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 14753602 0.05919183647690892 1.4947628884660051 chr2 243199373 15609825 0.06418530116851905 0.7167481154317016 chr3 198022430 8482889 0.04283802092520529 0.2781679465194898 chr4 191154276 15097388 0.07898012179439816 0.3781532192204322 chr5 180915260 9368089 0.051781640752692724 0.30902778459266866 chr6 171115067 27019296 0.15790132612927651 0.5652453784974453 chr7 159138663 9032731 0.05676012874382387 0.459202555856298 chr8 146364022 8889298 0.060734174140144905 1.256772083305837 chr9 141213431 7263072 0.05143329461345642 0.7228763334596497 chr10 135534747 9372792 0.06915416310180592 0.44749371134655513 chr11 135006516 5437589 0.0402764930249737 0.34854012034110177 chr12 133851895 2075854 0.015508588802571678 0.2466687996819866 chr13 115169878 7569142 0.06572154222478208 0.33325379792969356 chr14 107349540 2474861 0.02305423013456788 0.328585327932755 chr15 102531392 5494393 0.05358742227941273 0.3066035367867714 chr16 90354753 8152647 0.09022930979624282 0.4649145934007711 chr17 81195210 8983066 0.11063541802527514 0.44377038930777324 chr18 78077248 4075208 0.05219456505434208 1.296429758200151 chr19 59128983 6597917 0.111585159514751 1.222100511197512 chr20 63025520 4739920 0.07520636085192157 0.40515869640510765 chr21 48129895 3156435 0.06558158915576276 0.37184980503489007 chr22 51304566 2264782 0.04414386820853333 0.26908020120291193 chrMT 16571 87748 5.295274877798564 4.680938200824265 chrX 155270560 4997119 0.032183299912101816 0.29626659046565573 chrY 59373566 639394 0.01076900114101282 0.3282596515916752