BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716769.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 = 1,489,130 number of mapped reads = 1,387,606 (93.18%) number of supplementary alignments = 29,138 (1.96%) number of secondary alignments = 0 number of mapped bases = 106,780,921 bp number of sequenced bases = 106,739,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,212 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1386 >>>>>>> ACTG content number of A's = 26,770,353 bp (25.08%) number of C's = 22,400,962 bp (20.99%) number of T's = 31,358,181 bp (29.38%) number of G's = 26,206,142 bp (24.55%) number of N's = 3,719 bp (0%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 698,347 number of insertions = 8,926 mapped reads with insertion percentage = 0.63% number of deletions = 19,767 mapped reads with deletion percentage = 1.4% homopolymer indels = 39.25% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.298X There is a 2.93% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 12069266 0.04842221035028033 0.5365668383495248 chr2 243199373 10091707 0.041495612737455535 0.3199638544326994 chr3 198022430 6943991 0.03506668916243478 0.21480799997333586 chr4 191154276 5113714 0.026751763585973875 0.26022146913764893 chr5 180915260 5491181 0.030352226782859554 0.20146674971873724 chr6 171115067 6680339 0.03904003964770677 0.23758457632536104 chr7 159138663 6606560 0.04151448727453491 0.3888786788048249 chr8 146364022 6743015 0.04607016743499984 0.32248888446552076 chr9 141213431 3159252 0.02237217789857397 0.21452038797047837 chr10 135534747 5504395 0.04061242686349649 0.42242988577715984 chr11 135006516 3252268 0.02408971134400654 0.23055445098878302 chr12 133851895 3812960 0.028486410296992806 0.19208092124875087 chr13 115169878 2035002 0.01766956807925072 0.1500150727829292 chr14 107349540 1923768 0.017920598448768386 0.1643907139538883 chr15 102531392 2264637 0.022087254994060748 0.16854038477274536 chr16 90354753 3322938 0.03677657112293805 0.23146288896364856 chr17 81195210 2516737 0.030996126495639337 0.2258485470467234 chr18 78077248 3148717 0.040328227244894696 0.31385680414401046 chr19 59128983 2784951 0.04709959242830204 0.39958119202220665 chr20 63025520 2921625 0.0463562220510041 0.2586360918823938 chr21 48129895 1701223 0.03534649306839335 0.25624024150528446 chr22 51304566 1462542 0.028507053348818895 0.20027433014191423 chrMT 16571 35477 2.1409088166073262 2.026145960999988 chrX 155270560 6823435 0.043945452376806006 0.2523790081356405 chrY 59373566 371221 0.006252294160670761 0.21502039095620484