BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716976.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 = 2,602,714 number of mapped reads = 2,274,636 (87.39%) number of supplementary alignments = 9,210 (0.35%) number of secondary alignments = 0 number of mapped bases = 129,564,541 bp number of sequenced bases = 129,526,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,334 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3368 >>>>>>> ACTG content number of A's = 30,648,403 bp (23.66%) number of C's = 25,896,036 bp (19.99%) number of T's = 39,786,690 bp (30.72%) number of G's = 33,193,548 bp (25.63%) number of N's = 1,874 bp (0%) GC percentage = 45.62% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 656,434 number of insertions = 7,523 mapped reads with insertion percentage = 0.33% number of deletions = 23,775 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.47% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.341X There is a 3.66% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 10763757 0.043184474152222874 0.4149697453899908 chr2 243199373 12675890 0.0521213925991495 0.5044800730310128 chr3 198022430 9303517 0.04698213732656447 0.25760960343897343 chr4 191154276 7218663 0.03776354445767146 0.232184002872855 chr5 180915260 6954527 0.038440798194690706 0.21933594337859588 chr6 171115067 7083318 0.0413950572803738 0.26617944521827597 chr7 159138663 6305849 0.03962487104720743 0.6947390928291587 chr8 146364022 10411024 0.07113103246096913 0.36210970040353807 chr9 141213431 5437301 0.038504134921840405 0.26004185710612565 chr10 135534747 6175489 0.045563880382644605 0.4038486295626588 chr11 135006516 3901219 0.02889652377963742 0.25010815603274267 chr12 133851895 6038033 0.04510980587910242 0.24644846523882735 chr13 115169878 3384159 0.029384063426723436 0.19188186992295825 chr14 107349540 4144578 0.038608251139222394 0.22581805544281822 chr15 102531392 3125007 0.03047853870939351 0.2031523896641208 chr16 90354753 3589590 0.03972773850646241 0.23651314953841784 chr17 81195210 5692112 0.07010403692533095 0.3168523022776553 chr18 78077248 3086052 0.03952562467365653 0.39765533405654746 chr19 59128983 2850544 0.0482089130469232 0.38184583896942814 chr20 63025520 2991386 0.04746309114149316 0.24861071487435518 chr21 48129895 1397432 0.029034594818875048 0.20008847923070733 chr22 51304566 2063738 0.04022523063541752 0.23004612902134963 chrMT 16571 108693 6.559229980085692 4.288948559796936 chrX 155270560 4571767 0.029443875258774104 0.2251925945493832 chrY 59373566 290896 0.004899419381345564 0.11641743383109263