BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004144.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,027,254 number of mapped reads = 2,348,777 (77.59%) number of supplementary alignments = 13,600 (0.45%) number of secondary alignments = 0 number of mapped bases = 153,846,355 bp number of sequenced bases = 153,771,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,121 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8009 >>>>>>> ACTG content number of A's = 41,709,018 bp (27.12%) number of C's = 27,362,259 bp (17.79%) number of T's = 49,689,171 bp (32.31%) number of G's = 34,995,189 bp (22.76%) number of N's = 15,477 bp (0.01%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,526,496 number of insertions = 14,212 mapped reads with insertion percentage = 0.6% number of deletions = 45,443 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.4941X There is a 4.22% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12680371 0.05087397956773797 0.8670486152581124 chr2 243199373 11292626 0.04643361477745257 0.5673291008983731 chr3 198022430 9387263 0.04740504901389201 0.2476705605578454 chr4 191154276 11417366 0.059728540940407734 0.29498541476220524 chr5 180915260 4966299 0.02745096792829969 0.19773792732546844 chr6 171115067 11971311 0.06996058973579457 0.36617601163627705 chr7 159138663 10300391 0.0647258862543039 0.8122711870813533 chr8 146364022 11656710 0.07964190817330778 0.7779635497567711 chr9 141213431 5590364 0.0395880474003921 0.4180060071744924 chr10 135534747 6917857 0.05104120642952172 0.41257243897988477 chr11 135006516 7555858 0.055966617196461836 0.4817350392086551 chr12 133851895 6515414 0.04867629255454321 0.26069479944523194 chr13 115169878 7066223 0.06135478410422559 0.28218203608456105 chr14 107349540 3396222 0.03163704287880507 0.26133159445182186 chr15 102531392 4434408 0.04324927140363022 0.24483463364961067 chr16 90354753 5333590 0.05902943478800722 0.32802484363879986 chr17 81195210 3130952 0.038560796874593954 0.2706230006911473 chr18 78077248 3398800 0.04353124741281865 0.8908325700284789 chr19 59128983 3222585 0.05450093738294129 0.6215354734360825 chr20 63025520 2806173 0.04452439265871983 0.2705990932768399 chr21 48129895 1968326 0.04089612079976489 0.25850734819652593 chr22 51304566 1204358 0.023474674749222126 0.17013577273804129 chrMT 16571 36518 2.2037294067950035 2.185529924225819 chrX 155270560 7247195 0.046674623959622484 0.31149914052782113 chrY 59373566 349175 0.005880984140315911 0.13940478217265556