BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716412.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 = 2,274,525 number of mapped reads = 1,851,988 (81.42%) number of supplementary alignments = 9,744 (0.43%) number of secondary alignments = 0 number of mapped bases = 107,312,940 bp number of sequenced bases = 107,282,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,035 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.215 >>>>>>> ACTG content number of A's = 26,486,343 bp (24.69%) number of C's = 22,115,193 bp (20.61%) number of T's = 34,116,996 bp (31.8%) number of G's = 24,562,962 bp (22.9%) number of N's = 1,406 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 530,942 number of insertions = 6,862 mapped reads with insertion percentage = 0.37% number of deletions = 19,362 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.31X There is a 3.05% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 11656169 0.046764854399299574 0.5826191477823138 chr2 243199373 9791831 0.04026256679535107 0.4038000878319472 chr3 198022430 9134534 0.04612878450183648 0.23933338712785104 chr4 191154276 5024924 0.026287269660658807 0.19424016316494522 chr5 180915260 4806045 0.026565172003732575 0.18355474365888833 chr6 171115067 8256966 0.04825388053057888 0.34206565337389677 chr7 159138663 5880761 0.03695369113412748 0.3720660234638241 chr8 146364022 8770795 0.05992452844729834 0.29974749788820115 chr9 141213431 3829817 0.02712077011994702 0.24294056696846103 chr10 135534747 5422871 0.04001092797258846 0.3199863948279489 chr11 135006516 3615085 0.02677711496532508 0.24561609184630165 chr12 133851895 4947841 0.036965042594279296 0.21904803927780972 chr13 115169878 2314218 0.020093951996719144 0.1568365895471769 chr14 107349540 2265686 0.021105688948457536 0.17932381469439448 chr15 102531392 3048284 0.02973025080943015 0.19907770825848609 chr16 90354753 2206608 0.024421604030061373 0.1936299971327772 chr17 81195210 2377006 0.029275199854769757 0.20118374000477873 chr18 78077248 2078390 0.026619662619256253 0.426749792236936 chr19 59128983 1960756 0.033160658284956464 0.40065088212725947 chr20 63025520 1630147 0.025864871880470007 0.1798053903635914 chr21 48129895 940357 0.019537898430902458 0.1723092658312029 chr22 51304566 1654489 0.03224837726918887 0.19985157369092227 chrMT 16571 73451 4.432502564721501 3.1246213621880505 chrX 155270560 5366864 0.034564594859450494 0.2394513986234593 chrY 59373566 259045 0.004362968530473645 0.10016199549090216