BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716147.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,699,405 number of mapped reads = 2,451,662 (90.82%) number of supplementary alignments = 14,438 (0.53%) number of secondary alignments = 0 number of mapped bases = 142,509,881 bp number of sequenced bases = 142,468,382 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,514 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5956 >>>>>>> ACTG content number of A's = 36,458,540 bp (25.59%) number of C's = 26,365,453 bp (18.51%) number of T's = 43,735,685 bp (30.7%) number of G's = 35,907,666 bp (25.2%) number of N's = 1,038 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 706,992 number of insertions = 11,750 mapped reads with insertion percentage = 0.48% number of deletions = 26,362 mapped reads with deletion percentage = 1.07% homopolymer indels = 39.07% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3719X There is a 3.84% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17011816 0.0682518500124419 0.6261634052942145 chr2 243199373 14695355 0.060425135224341224 0.5426364065499107 chr3 198022430 9099584 0.04595228934419197 0.25005262701730196 chr4 191154276 6034390 0.03156816643745913 0.24240248114805146 chr5 180915260 10346094 0.05718751419863642 0.2810797824098914 chr6 171115067 5505665 0.032175220432225295 0.23999950556264826 chr7 159138663 7496076 0.047104052897566445 0.4912085819416287 chr8 146364022 6373312 0.04354425297222291 0.3246342021577369 chr9 141213431 3968543 0.02810315542860792 0.2839618447782247 chr10 135534747 6469633 0.0477341282822478 0.32238727954090607 chr11 135006516 6231569 0.046157542499652385 0.3763064485316597 chr12 133851895 5745120 0.042921469285137875 0.24561818220032572 chr13 115169878 4200966 0.03647625640447409 0.2259821179106463 chr14 107349540 3165342 0.02948631172522956 0.21836618333945695 chr15 102531392 6309714 0.06153933811802731 0.29445704948375284 chr16 90354753 4304197 0.0476366417602846 0.27681849900197936 chr17 81195210 5493327 0.06765580137054883 0.3396089964073806 chr18 78077248 4650454 0.05956221715191601 0.6524748912344793 chr19 59128983 2283381 0.03861695033719758 0.46178752067825707 chr20 63025520 3821159 0.060628758001520656 0.29354245707880294 chr21 48129895 1841185 0.038254498581391044 0.2442372179046027 chr22 51304566 1717030 0.0334673915768043 0.21299566837893938 chrMT 16571 2695 0.1626335163840444 0.47320978886244514 chrX 155270560 5394507 0.03474262603290669 0.2548801164784577 chrY 59373566 348767 0.005874112395405053 0.13997096177937335