BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716607.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 = 1,005,673 number of mapped reads = 851,941 (84.71%) number of supplementary alignments = 27,452 (2.73%) number of secondary alignments = 0 number of mapped bases = 64,233,564 bp number of sequenced bases = 64,210,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,071 duplication rate = 1.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4665 >>>>>>> ACTG content number of A's = 16,266,910 bp (25.33%) number of C's = 13,169,370 bp (20.51%) number of T's = 19,290,227 bp (30.04%) number of G's = 15,475,421 bp (24.1%) number of N's = 8,117 bp (0.01%) GC percentage = 44.61% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 498,544 number of insertions = 5,332 mapped reads with insertion percentage = 0.62% number of deletions = 13,441 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2084X There is a 1.91% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5640907 0.022631466181983955 0.23253536310092904 chr2 243199373 5161404 0.021222933004847837 0.3374056137221941 chr3 198022430 5249766 0.02651096645970863 0.1752465058857289 chr4 191154276 2876817 0.015049713039116112 0.13231460672173195 chr5 180915260 4050005 0.0223861989309249 0.1602991529458495 chr6 171115067 4258781 0.02488840447930865 0.18546460875749235 chr7 159138663 3205097 0.020140278544378623 0.2673011935496741 chr8 146364022 4464486 0.030502619011111898 0.27873067102552196 chr9 141213431 2638001 0.018680949689551838 0.19625778114526896 chr10 135534747 2939137 0.0216854870434074 0.1803201888864621 chr11 135006516 2734975 0.02025809628329347 0.1750169906563015 chr12 133851895 2663122 0.019896035091621227 0.15139895875999565 chr13 115169878 1672813 0.014524744048092158 0.126204547776333 chr14 107349540 1431269 0.013332791179170399 0.13816932600943982 chr15 102531392 1637911 0.015974727037744694 0.1330178096363117 chr16 90354753 1764810 0.019532010673528152 0.15794929545636308 chr17 81195210 2179393 0.026841398649008974 0.19700301671632722 chr18 78077248 2162858 0.027701514274683453 0.3671447339097765 chr19 59128983 1271897 0.021510550925592616 0.23363553006665547 chr20 63025520 1108172 0.017582909272307472 0.15439492904708632 chr21 48129895 1446377 0.03005153034304355 0.18896487773756976 chr22 51304566 1022917 0.019938127924130574 0.15239280418310103 chrMT 16571 2796 0.1687285015991793 0.5415696030951167 chrX 155270560 2511766 0.016176704714660654 0.1574275446956829 chrY 59373566 138087 0.002325731959572716 0.07664685683780739