BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524757.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 = 1,401,616 number of mapped reads = 1,263,453 (90.14%) number of supplementary alignments = 4,508 (0.32%) number of secondary alignments = 0 number of mapped bases = 71,943,636 bp number of sequenced bases = 71,921,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,961 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1844 >>>>>>> ACTG content number of A's = 17,697,980 bp (24.61%) number of C's = 14,003,597 bp (19.47%) number of T's = 22,508,343 bp (31.3%) number of G's = 17,703,621 bp (24.62%) number of N's = 8,388 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 367,768 number of insertions = 4,054 mapped reads with insertion percentage = 0.32% number of deletions = 13,594 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2082X There is a 2.12% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5800035 0.02326989187320821 0.25637080196008466 chr2 243199373 6040584 0.024837991667026212 0.3122467615406535 chr3 198022430 4696813 0.023718590868721287 0.16800463600156115 chr4 191154276 4526224 0.023678382167082675 0.1864922048698326 chr5 180915260 4244302 0.023460165825702043 0.16465129949181756 chr6 171115067 4084255 0.02386847091612336 0.17665382037222477 chr7 159138663 3918712 0.024624512523396026 0.25334770683571645 chr8 146364022 3587066 0.02450783977499607 0.19352137273178271 chr9 141213431 3061580 0.021680515644436116 0.1837304510821858 chr10 135534747 3532865 0.026066120151461973 0.25347525452771796 chr11 135006516 3267334 0.024201305957706514 0.1966751424406678 chr12 133851895 3255737 0.02432342851776585 0.17015523580672767 chr13 115169878 2218290 0.019261025873449307 0.14947444440564225 chr14 107349540 2153820 0.020063616481262984 0.15543931863708213 chr15 102531392 2101796 0.020499048720610365 0.15841645214603955 chr16 90354753 2191534 0.02425477274006825 0.18373675004700937 chr17 81195210 2094067 0.0257905238498675 0.1798097449088892 chr18 78077248 1904853 0.024397030489599222 0.28210243925766504 chr19 59128983 1614188 0.027299437908478826 0.2320901533041796 chr20 63025520 1559665 0.024746562979567642 0.17712991824677535 chr21 48129895 953679 0.019814691056359048 0.16604184796541988 chr22 51304566 927004 0.018068645196218987 0.14588466694940963 chrMT 16571 19293 1.1642628688672982 1.2657519256351917 chrX 155270560 3953837 0.025464176853616037 0.18497339267906712 chrY 59373566 236103 0.003976567619334167 0.10953732508139177