BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716195.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 = 4,535,394 number of mapped reads = 3,264,747 (71.98%) number of supplementary alignments = 87,943 (1.94%) number of secondary alignments = 0 number of mapped bases = 243,928,443 bp number of sequenced bases = 243,845,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,278 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8184 >>>>>>> ACTG content number of A's = 62,839,198 bp (25.77%) number of C's = 48,694,843 bp (19.97%) number of T's = 74,283,352 bp (30.46%) number of G's = 57,997,855 bp (23.78%) number of N's = 29,933 bp (0.01%) GC percentage = 43.75% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,785,681 number of insertions = 20,236 mapped reads with insertion percentage = 0.61% number of deletions = 47,819 mapped reads with deletion percentage = 1.45% homopolymer indels = 40.7% >>>>>>> Coverage mean coverageData = 0.0788X std coverageData = 0.5645X There is a 6.22% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 19571644 0.07852194679185975 0.6218409297311303 chr2 243199373 20646184 0.08489406755172843 0.8843806930979919 chr3 198022430 16006833 0.08083343386908241 0.34533455707793453 chr4 191154276 15322784 0.08015925314691888 0.395369171838967 chr5 180915260 14718428 0.08135537046460316 0.3524875472743887 chr6 171115067 14150753 0.08269729397937822 0.4240484019654875 chr7 159138663 13346993 0.08387020946631932 0.7148584646817806 chr8 146364022 12524645 0.08557188323234244 0.7648564739665501 chr9 141213431 10487105 0.07426421782783538 0.6220408842457787 chr10 135534747 11620500 0.08573816129969977 0.5558230346317885 chr11 135006516 11145069 0.08255208215283476 0.6316186820252889 chr12 133851895 11047302 0.08253377361598056 0.3622684691418706 chr13 115169878 7767624 0.06744492687575826 0.31615662399136824 chr14 107349540 7283257 0.06784618732413758 0.4116980587654989 chr15 102531392 7009513 0.06836455512083557 0.3205176743496487 chr16 90354753 7316836 0.08097898292079886 0.4047095606164774 chr17 81195210 6874833 0.08467042575541094 0.41081578985507966 chr18 78077248 6563076 0.0840587516609192 1.176633233763136 chr19 59128983 4876245 0.08246793285790151 0.5932424570452824 chr20 63025520 5226509 0.08292686835427934 0.38049991467364835 chr21 48129895 3221847 0.06694066130831991 0.35973274561426655 chr22 51304566 2847233 0.05549667840480319 0.29056964392832074 chrMT 16571 10642 0.6422062639551023 1.087495677809391 chrX 155270560 13713915 0.08832269942222144 0.47735671899427956 chrY 59373566 628673 0.010588432569470393 0.29734286977941354