BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524531.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 = 1,457,145 number of mapped reads = 1,330,374 (91.3%) number of supplementary alignments = 5,779 (0.4%) number of secondary alignments = 0 number of mapped bases = 77,143,020 bp number of sequenced bases = 77,119,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,292 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2365 >>>>>>> ACTG content number of A's = 18,949,877 bp (24.57%) number of C's = 14,438,041 bp (18.72%) number of T's = 24,894,857 bp (32.28%) number of G's = 18,835,774 bp (24.42%) number of N's = 1,135 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 397,983 number of insertions = 4,371 mapped reads with insertion percentage = 0.33% number of deletions = 14,009 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2512X There is a 2.2% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 6239533 0.025033169325584147 0.4597443302510651 chr2 243199373 6534398 0.026868482099252782 0.31317438284520305 chr3 198022430 5027975 0.025390936774182603 0.17624787128698086 chr4 191154276 5049839 0.02641760940780629 0.208691128828899 chr5 180915260 4630357 0.025594065420462598 0.17768368480797284 chr6 171115067 4351767 0.025431816591580447 0.1931876088787092 chr7 159138663 4184454 0.02629438956641228 0.29224216166933525 chr8 146364022 3992491 0.027277816948758075 0.2453648419273648 chr9 141213431 3214297 0.022761977931121863 0.20833674485813328 chr10 135534747 3744181 0.02762524801112441 0.25904291188775447 chr11 135006516 3517002 0.026050609290591574 0.22076520467265967 chr12 133851895 3488302 0.02606090858855603 0.18212345749951464 chr13 115169878 2376543 0.020635109121154058 0.15890117607348436 chr14 107349540 2322127 0.021631457386775948 0.16508544413537057 chr15 102531392 2174231 0.021205515282578042 0.1624693254614554 chr16 90354753 2232960 0.02471325443167334 0.1874704575517354 chr17 81195210 2108779 0.02597171680447652 0.18669422436706645 chr18 78077248 2057242 0.0263488026627168 0.35942871999593773 chr19 59128983 1610870 0.027243323295447174 0.32250029177985673 chr20 63025520 1672651 0.02653926536425245 0.18496984882031658 chr21 48129895 1048286 0.021780350860935806 0.18192258565139713 chr22 51304566 917083 0.01787527059482386 0.15036677897104986 chrMT 16571 5790 0.34940558807555366 0.6622050334901883 chrX 155270560 4360501 0.028083243855113293 0.2021113764254717 chrY 59373566 281361 0.004738826029078327 0.15989106109763077