BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717057.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 = 3,267,504 number of mapped reads = 2,928,885 (89.64%) number of supplementary alignments = 16,580 (0.51%) number of secondary alignments = 0 number of mapped bases = 169,414,022 bp number of sequenced bases = 169,370,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,617 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7806 >>>>>>> ACTG content number of A's = 43,478,779 bp (25.67%) number of C's = 33,745,011 bp (19.92%) number of T's = 52,316,780 bp (30.89%) number of G's = 39,825,577 bp (23.51%) number of N's = 4,605 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 837,257 number of insertions = 13,486 mapped reads with insertion percentage = 0.46% number of deletions = 28,071 mapped reads with deletion percentage = 0.95% homopolymer indels = 40.11% >>>>>>> Coverage mean coverageData = 0.0547X std coverageData = 0.4707X There is a 4.51% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 18865340 0.0756882367005216 0.911302367750337 chr2 243199373 13925142 0.05725813281599209 0.567128502347231 chr3 198022430 15899180 0.08028979343400644 0.34266586633628343 chr4 191154276 7673494 0.04014293669266389 0.2605741817182728 chr5 180915260 7281212 0.04024653310063507 0.24211964766607277 chr6 171115067 12234614 0.07149933792796867 0.46444594924130717 chr7 159138663 9597479 0.06030890808728235 0.6211341291317103 chr8 146364022 13283244 0.09075484411052875 0.42434661465629964 chr9 141213431 6152705 0.04357025359719501 0.37055361028759487 chr10 135534747 8902981 0.06568781214458606 0.5341556839779988 chr11 135006516 5511334 0.04082272591939192 0.37121173727545237 chr12 133851895 7432642 0.05552885149664859 0.2906388335872635 chr13 115169878 3758524 0.032634609546082875 0.21453608329372711 chr14 107349540 3717301 0.03462801051592769 0.27121640394046664 chr15 102531392 4958787 0.048363597755504965 0.26991832970731616 chr16 90354753 3596524 0.03980448045715979 0.28367570177250057 chr17 81195210 3751769 0.0462067774687694 0.27189379048259266 chr18 78077248 3173852 0.040650152013554576 0.7023727428618587 chr19 59128983 3335458 0.056409865868993554 0.6409195589898726 chr20 63025520 2554333 0.04052855097427201 0.24183632919174758 chr21 48129895 1549024 0.03218423809152295 0.23842552769437847 chr22 51304566 2687747 0.052388066200579494 0.2718002136789875 chrMT 16571 424931 25.643051113390865 14.407184027838717 chrX 155270560 8739024 0.05628255607502156 0.3392541235341492 chrY 59373566 407381 0.0068613193959075995 0.14183307975967485