BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238646.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 = 2,922,071 number of mapped reads = 2,638,164 (90.28%) number of supplementary alignments = 13,038 (0.45%) number of secondary alignments = 0 number of mapped bases = 161,420,805 bp number of sequenced bases = 161,354,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 308,526 duplication rate = 9.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.298 >>>>>>> ACTG content number of A's = 39,143,292 bp (24.26%) number of C's = 28,127,240 bp (17.43%) number of T's = 54,501,840 bp (33.78%) number of G's = 39,574,903 bp (24.53%) number of N's = 7,711 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 917,393 number of insertions = 11,104 mapped reads with insertion percentage = 0.42% number of deletions = 38,850 mapped reads with deletion percentage = 1.46% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.0521X std coverageData = 0.7596X There is a 3.97% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13705128 0.05498533141066878 0.7464730501217022 chr2 243199373 15752964 0.06477386765302227 2.0141580599808697 chr3 198022430 10987559 0.05548643656175717 0.3186615005775025 chr4 191154276 8785214 0.045958762648866926 0.3021565456144183 chr5 180915260 9157465 0.0506174271866287 0.3030990713396031 chr6 171115067 14368345 0.08396890613963293 0.7520163548064925 chr7 159138663 10089440 0.06340030643590364 0.9125101716346042 chr8 146364022 9038865 0.06175605778310738 0.5736078067680366 chr9 141213431 5828923 0.041277398040134014 0.49561897462502974 chr10 135534747 8899660 0.06566330920291606 0.4446219034971084 chr11 135006516 4780036 0.035405965146156355 0.31441852136724063 chr12 133851895 4968484 0.03711926528944547 0.28113306615722283 chr13 115169878 4636181 0.0402551524800608 0.4463838274932033 chr14 107349540 3262295 0.030389464174695114 0.28546087711998647 chr15 102531392 4029710 0.03930220707429779 0.4585482665037528 chr16 90354753 3983153 0.044083491656493154 0.36057436078127914 chr17 81195210 3279646 0.040392111800683805 0.2717637393484824 chr18 78077248 7087840 0.09077983896153717 1.2316501792997017 chr19 59128983 2586296 0.04373990332287636 0.527473656445368 chr20 63025520 4093725 0.06495345060223223 0.34600385353696206 chr21 48129895 3003640 0.062406951022851806 0.3632249684448531 chr22 51304566 1188086 0.02315750999628376 0.18855375703504215 chrMT 16571 64162 3.871944964093899 3.6179857803641946 chrX 155270560 7417355 0.04777051747607531 0.3169767955530191 chrY 59373566 426633 0.0071855714376327 0.29337276890663483