BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524385.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 = 1,184,321 number of mapped reads = 1,095,220 (92.48%) number of supplementary alignments = 4,468 (0.38%) number of secondary alignments = 0 number of mapped bases = 64,403,789 bp number of sequenced bases = 64,386,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,068 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7728 >>>>>>> ACTG content number of A's = 16,635,900 bp (25.84%) number of C's = 12,622,763 bp (19.6%) number of T's = 19,996,444 bp (31.06%) number of G's = 15,122,392 bp (23.49%) number of N's = 8,727 bp (0.01%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 312,174 number of insertions = 4,744 mapped reads with insertion percentage = 0.43% number of deletions = 11,093 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.22% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.2278X There is a 1.91% of reference with a coverageData >= 1X There is a 0.12% 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 5413171 0.021717783403235734 0.46788537961515286 chr2 243199373 5296971 0.021780364540660225 0.24344326378003384 chr3 198022430 4436865 0.022405870890484476 0.15866390146916523 chr4 191154276 4278061 0.02238014806427872 0.1716839210636053 chr5 180915260 4013667 0.02218534246364845 0.15855429612787275 chr6 171115067 2519429 0.014723595321971268 0.13898146740545259 chr7 159138663 3678686 0.023116230403418685 0.31242121064954553 chr8 146364022 3402403 0.02324617042841307 0.20769018084560603 chr9 141213431 2414704 0.017099676588128505 0.17111472973617922 chr10 135534747 3170804 0.023394768280343637 0.20793679525297334 chr11 135006516 2655463 0.019669146932137706 0.19303963976444385 chr12 133851895 3001108 0.022421109540511176 0.16226674567515012 chr13 115169878 2068425 0.017959774169423015 0.14171770085790975 chr14 107349540 1823944 0.01699070159033751 0.14102360277121329 chr15 102531392 1946066 0.0189801968162102 0.14571506708211004 chr16 90354753 1977010 0.02188053128760144 0.16282932649893883 chr17 81195210 1672585 0.020599552609076324 0.1629596946079001 chr18 78077248 1752719 0.02244852431274217 0.2898971838064907 chr19 59128983 1748554 0.02957185987792146 0.30752759158474535 chr20 63025520 1801786 0.028588197288971197 0.18397675041904998 chr21 48129895 880934 0.018303260374866806 0.15660525138863068 chr22 51304566 440970 0.008595141414898626 0.09829010781469955 chrMT 16571 27188 1.6406976042483858 1.5744083188940035 chrX 155270560 3783522 0.024367285079669964 0.17985714588224636 chrY 59373566 198754 0.0033475166372860274 0.09689988656433524