BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524684.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 = 1,349,428 number of mapped reads = 1,243,237 (92.13%) number of supplementary alignments = 5,152 (0.38%) number of secondary alignments = 0 number of mapped bases = 74,367,891 bp number of sequenced bases = 74,345,664 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,813 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2115 >>>>>>> ACTG content number of A's = 19,239,113 bp (25.88%) number of C's = 14,029,129 bp (18.87%) number of T's = 22,404,052 bp (30.13%) number of G's = 18,663,622 bp (25.1%) number of N's = 9,748 bp (0.01%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 375,509 number of insertions = 4,515 mapped reads with insertion percentage = 0.36% number of deletions = 13,891 mapped reads with deletion percentage = 1.11% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2354X There is a 2.2% of reference with a coverageData >= 1X There is a 0.14% 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 5969978 0.02395170762683877 0.4064116077727723 chr2 243199373 6275231 0.025802825568962302 0.2833877813005432 chr3 198022430 4953203 0.025013343185415916 0.16985744513591847 chr4 191154276 4799293 0.02510690893464502 0.1853239053352804 chr5 180915260 4505940 0.024906356710871155 0.16906629726525904 chr6 171115067 4358350 0.025470287780093612 0.18617667422129522 chr7 159138663 4120950 0.02589534134768997 0.2695802145802255 chr8 146364022 3816444 0.026075014527818866 0.2735382457439317 chr9 141213431 3135919 0.0222069457401683 0.20242069014002903 chr10 135534747 3602572 0.026580431068351795 0.25596688312533217 chr11 135006516 3392414 0.02512777975842292 0.2083935291369327 chr12 133851895 3337969 0.024937779177500626 0.17034915799560818 chr13 115169878 2349551 0.0204007422843671 0.15302896713911818 chr14 107349540 2234543 0.020815580579106346 0.15671806787932818 chr15 102531392 2117802 0.020655157007914222 0.153623832279762 chr16 90354753 2124308 0.02351074989934398 0.17592569904180957 chr17 81195210 1996657 0.02459082253743786 0.1745497869758036 chr18 78077248 1972344 0.025261443641046363 0.3668142333614233 chr19 59128983 1482013 0.02506407052527861 0.3195004119967146 chr20 63025520 1558582 0.024729379464064716 0.17086699828191232 chr21 48129895 1000157 0.020780369456446974 0.17126779544357568 chr22 51304566 871537 0.016987513353099996 0.13877221324392403 chrMT 16571 16233 0.9796029207651922 1.0858102616760061 chrX 155270560 4135199 0.02663221540516116 0.1869004930394465 chrY 59373566 240702 0.004054026332189648 0.14050409191763388