BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238516.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 = 2,664,592 number of mapped reads = 2,086,414 (78.3%) number of supplementary alignments = 19,974 (0.75%) number of secondary alignments = 0 number of mapped bases = 125,482,866 bp number of sequenced bases = 125,423,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 958,156 duplication rate = 22.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3846 >>>>>>> ACTG content number of A's = 31,355,915 bp (25%) number of C's = 21,163,627 bp (16.87%) number of T's = 43,332,239 bp (34.55%) number of G's = 29,569,297 bp (23.58%) number of N's = 2,624 bp (0%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 748,147 number of insertions = 7,791 mapped reads with insertion percentage = 0.37% number of deletions = 34,347 mapped reads with deletion percentage = 1.63% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 1.0658X There is a 0.97% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 10070378 0.04040261949838833 0.9290837336272203 chr2 243199373 8809254 0.03622235489891662 1.8354856882284192 chr3 198022430 5188541 0.02620178431301949 0.5392168253396237 chr4 191154276 8078812 0.04226330777973285 0.6717207288239512 chr5 180915260 5292161 0.029252153743139192 0.5548888664206174 chr6 171115067 9908139 0.057903369783328315 1.0790527903635734 chr7 159138663 8699315 0.05466499991897004 1.1330720742742897 chr8 146364022 3825741 0.02613853423623464 0.687832260145549 chr9 141213431 4042807 0.0286290544133865 0.558735150626498 chr10 135534747 9101675 0.06715381259390259 0.8901300635948048 chr11 135006516 7993334 0.05920702375580154 0.8079550824872911 chr12 133851895 3401305 0.025410958881082708 0.5169294413214701 chr13 115169878 2618842 0.022738949154743397 0.7692170171422218 chr14 107349540 2766207 0.025768224065049555 0.5463372549438252 chr15 102531392 2242895 0.021875202864699232 0.5776157967220651 chr16 90354753 2288952 0.02533294513018037 0.5342752213456319 chr17 81195210 4524318 0.05572148898931353 0.8037931922944271 chr18 78077248 7977250 0.10217124968339047 3.7558157949598825 chr19 59128983 1559468 0.02637400342231491 0.6749560282933619 chr20 63025520 2421825 0.03842610104605246 0.6378363108812258 chr21 48129895 2371987 0.04928302877037234 0.7268327854320554 chr22 51304566 762619 0.014864544415013666 0.3723021125133572 chrMT 16571 33770 2.0378975318327197 4.903139598276717 chrX 155270560 10995230 0.07081335959630725 0.8863507952000185 chrY 59373566 508041 0.008556686657493337 0.43683987951662806