BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251060.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,598,292 number of mapped reads = 1,517,717 (94.96%) number of supplementary alignments = 41,616 (2.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 760,789 number of mapped paired reads (second in pair) = 756,928 number of mapped paired reads (both in pair) = 1,510,540 number of mapped paired reads (singletons) = 7,177 number of mapped bases = 186,888,883 bp number of sequenced bases = 186,728,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 252,640 duplication rate = 15.08% >>>>>>> Insert size mean insert size = 94,827.5639 std insert size = 2,919,108.206 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.2622 >>>>>>> ACTG content number of A's = 54,775,319 bp (29.33%) number of C's = 37,945,601 bp (20.32%) number of T's = 54,876,939 bp (29.39%) number of G's = 39,125,121 bp (20.95%) number of N's = 5,841 bp (0%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,313,946 number of insertions = 31,453 mapped reads with insertion percentage = 1.94% number of deletions = 75,213 mapped reads with deletion percentage = 4.76% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.6667X There is a 3.7% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.05% 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 0.01% 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 16869257 0.06767989958187506 1.2513992288098108 chr2 243199373 16224484 0.06671268844101831 1.038651653644236 chr3 198022430 12288878 0.06205801029711634 0.36457170359512764 chr4 191154276 11466146 0.059983727489308164 0.43456419683257635 chr5 180915260 10732217 0.05932178965997672 0.36624322480213817 chr6 171115067 9747970 0.056967338825867395 0.37834602258005945 chr7 159138663 10713147 0.06731957399943721 0.9533382463841772 chr8 146364022 8427902 0.05758178741494272 0.4121454329843606 chr9 141213431 8698002 0.06159472182217568 0.8521258883816031 chr10 135534747 10745867 0.07928496004054222 0.7835929946119157 chr11 135006516 8535906 0.06322588163077995 0.448119929741816 chr12 133851895 8533555 0.06375371077114747 0.3757543793086239 chr13 115169878 5551076 0.04819902648503283 0.32210138971689994 chr14 107349540 5721164 0.053294723014183386 0.34851073118979886 chr15 102531392 5792454 0.05649444416008709 0.3512030366781352 chr16 90354753 5425457 0.06004617156111312 0.6813474440072531 chr17 81195210 5823452 0.07172162003152649 0.48215874768530914 chr18 78077248 4175686 0.053481470043616294 0.6248531909565445 chr19 59128983 3799252 0.06425363345079012 0.6554631047799218 chr20 63025520 3863924 0.06130729266493953 0.3754437669736022 chr21 48129895 2177807 0.045248530045619254 0.33908775411656056 chr22 51304566 2235036 0.04356407575887105 0.31390874514218037 chrMT 16571 80523 4.85927222255748 3.8135143105362985 chrX 155270560 8833785 0.05689285206416464 0.36172002879157567 chrY 59373566 425936 0.0071738322067433176 0.5185037978036425