BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238326.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 = 2,205,375 number of mapped reads = 2,001,939 (90.78%) number of supplementary alignments = 25,475 (1.16%) number of secondary alignments = 0 number of mapped bases = 131,676,822 bp number of sequenced bases = 131,610,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,019 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8184 >>>>>>> ACTG content number of A's = 37,053,594 bp (28.15%) number of C's = 24,553,746 bp (18.66%) number of T's = 41,308,914 bp (31.39%) number of G's = 28,653,536 bp (21.77%) number of N's = 41,150 bp (0.03%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,092,815 number of insertions = 9,613 mapped reads with insertion percentage = 0.48% number of deletions = 38,036 mapped reads with deletion percentage = 1.88% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.3924X There is a 3.52% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 14646037 0.05876028288812167 0.7710531756312073 chr2 243199373 11718417 0.04818440465304982 0.43953967668630517 chr3 198022430 8678557 0.04382613121149963 0.24256046028613856 chr4 191154276 8392267 0.043903108921298735 0.2598715069857941 chr5 180915260 7969961 0.04405355855553589 0.24545564657231314 chr6 171115067 8260160 0.04827254633281358 0.33777451181573237 chr7 159138663 4567329 0.02870031024453184 0.34373260631078756 chr8 146364022 5543748 0.037876439334251145 0.6260312058917521 chr9 141213431 5845436 0.04139433450915869 0.35153634162384817 chr10 135534747 6561863 0.0484146179872236 0.3891172989798588 chr11 135006516 4584961 0.03396103488812347 0.27841442214269396 chr12 133851895 6660029 0.049756703108312365 0.2664566193060425 chr13 115169878 2730829 0.02371131277919735 0.17806609622470226 chr14 107349540 2494274 0.023235069288606174 0.22106430853178188 chr15 102531392 2785533 0.027167611261924542 0.19295961160207772 chr16 90354753 3702651 0.04097903958632923 0.25894762587950126 chr17 81195210 3360002 0.04138177609245668 0.25089094146891433 chr18 78077248 3595032 0.04604455320966231 0.554410179601063 chr19 59128983 2516882 0.04256596126471514 0.518572293130987 chr20 63025520 2650117 0.04204831630107931 0.2466992479103003 chr21 48129895 1205500 0.025046803031670856 0.20776158201693826 chr22 51304566 1264235 0.024641763853922867 0.17957413366617225 chrMT 16571 4576 0.27614507271739785 0.5964298703220177 chrX 155270560 11593865 0.0746687910444839 0.35645731577735257 chrY 59373566 344561 0.005803272789779883 0.12429750529954679