BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173917.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,812,644 number of mapped reads = 5,649,829 (97.2%) number of supplementary alignments = 614,291 (10.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,828,496 number of mapped paired reads (second in pair) = 2,821,333 number of mapped paired reads (both in pair) = 5,535,606 number of mapped paired reads (singletons) = 114,223 number of mapped bases = 667,624,651 bp number of sequenced bases = 667,234,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,461,533 duplication rate = 65.18% >>>>>>> Insert size mean insert size = 1,031,533.6424 std insert size = 9,398,378.3437 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.517 >>>>>>> ACTG content number of A's = 199,859,185 bp (29.95%) number of C's = 131,091,673 bp (19.65%) number of T's = 199,860,260 bp (29.95%) number of G's = 136,415,623 bp (20.44%) number of N's = 8,126 bp (0%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 6,994,083 number of insertions = 70,604 mapped reads with insertion percentage = 1.21% number of deletions = 161,168 mapped reads with deletion percentage = 2.78% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.2157X std coverageData = 3.2421X There is a 4.42% of reference with a coverageData >= 1X There is a 3.51% of reference with a coverageData >= 2X There is a 2.74% of reference with a coverageData >= 3X There is a 2.25% of reference with a coverageData >= 4X There is a 1.73% of reference with a coverageData >= 5X There is a 1.4% of reference with a coverageData >= 6X There is a 1.04% of reference with a coverageData >= 7X There is a 0.84% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 59365004 0.23817394621456128 2.7021084500361647 chr2 243199373 56091968 0.23064191041314897 9.424443146830784 chr3 198022430 48705019 0.2459570817305898 1.4390923939333782 chr4 191154276 41215477 0.2156136805435626 1.7322771698274095 chr5 180915260 45700837 0.2526090778633046 1.4674786276243086 chr6 171115067 41116805 0.2402874610685218 1.4850398108463494 chr7 159138663 48402672 0.3041540697121478 3.437653439487504 chr8 146364022 28262397 0.19309661359264915 1.5089891427915811 chr9 141213431 26806258 0.18982796331887156 1.6135018316463112 chr10 135534747 26230629 0.19353434879691775 3.2177943985849327 chr11 135006516 33658675 0.24931148508417178 1.4772358010058877 chr12 133851895 23713404 0.17716151123598212 1.220047854718577 chr13 115169878 22234527 0.19305852698741247 1.2885577156717969 chr14 107349540 21324733 0.19864764208584407 1.3138357557434315 chr15 102531392 19054412 0.18583978651143251 1.2374337708097725 chr16 90354753 27345187 0.3026424852270915 2.5186899597234453 chr17 81195210 14938492 0.18398242950538585 1.4747727882917283 chr18 78077248 10246033 0.13122943318903862 2.280320645990123 chr19 59128983 12856029 0.21742347572593967 2.842233259825096 chr20 63025520 20477996 0.3249159388133569 1.6737337539204986 chr21 48129895 9706643 0.20167596459539336 1.395870717201876 chr22 51304566 6229444 0.12142084975438638 0.9628343312268154 chrMT 16571 1359044 82.01339689819564 65.7716586003926 chrX 155270560 21656954 0.13947881684718597 1.0785939697044518 chrY 59373566 926012 0.015596368255866593 0.753670402709956