BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716980.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 = 5,397,306 number of mapped reads = 4,634,018 (85.86%) number of supplementary alignments = 18,253 (0.34%) number of secondary alignments = 0 number of mapped bases = 260,279,092 bp number of sequenced bases = 260,203,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 224,656 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4896 >>>>>>> ACTG content number of A's = 61,368,899 bp (23.58%) number of C's = 50,680,261 bp (19.48%) number of T's = 81,320,375 bp (31.25%) number of G's = 66,830,077 bp (25.68%) number of N's = 3,814 bp (0%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,347,137 number of insertions = 16,993 mapped reads with insertion percentage = 0.36% number of deletions = 47,019 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.99% >>>>>>> Coverage mean coverageData = 0.0841X std coverageData = 0.6106X There is a 6.72% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 21955501 0.08808604332424111 0.8169501259468299 chr2 243199373 25567339 0.10512913205578042 0.9996114389851429 chr3 198022430 17341821 0.08757503379793895 0.3831377279812992 chr4 191154276 14573942 0.07624177865631424 0.38987694599336536 chr5 180915260 14263852 0.0788427244888021 0.34363552317460183 chr6 171115067 14466016 0.08453969748905864 0.44474958637646445 chr7 159138663 12873450 0.08089454666337118 1.2482055861667616 chr8 146364022 20227715 0.13820141537241987 0.5900134933853933 chr9 141213431 10646278 0.07539139814540728 0.4400990097271265 chr10 135534747 12462265 0.09194885648032382 0.7152302983424464 chr11 135006516 7871773 0.05830661536366141 0.42770326410164633 chr12 133851895 12303715 0.09192036466872583 0.3795681508614367 chr13 115169878 6739515 0.05851803541894869 0.29641008510145456 chr14 107349540 8529069 0.07945137911163848 0.36798873729989934 chr15 102531392 6402111 0.06244049627259523 0.3219905223144249 chr16 90354753 7418761 0.08210703647211565 0.38705686027117553 chr17 81195210 11873154 0.146229734488032 0.5267643757451491 chr18 78077248 6082307 0.07790114477395514 0.7250960230032638 chr19 59128983 5933625 0.10035053367990449 0.7156935027512844 chr20 63025520 5969607 0.09471729864347014 0.3864218484142585 chr21 48129895 2705913 0.0562210451529138 0.32253957584215004 chr22 51304566 4170432 0.08128773567639185 0.3611074349069904 chrMT 16571 54750 3.303964757709251 2.7785659504770472 chrX 155270560 9213220 0.059336554205768305 0.38077592233867746 chrY 59373566 632961 0.01066065326108255 0.25430428373087915