BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237587.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 = 2,088,496 number of mapped reads = 1,803,873 (86.37%) number of supplementary alignments = 16,395 (0.79%) number of secondary alignments = 0 number of mapped bases = 117,879,336 bp number of sequenced bases = 117,807,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,240 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5512 >>>>>>> ACTG content number of A's = 32,779,679 bp (27.82%) number of C's = 20,561,476 bp (17.45%) number of T's = 38,402,069 bp (32.6%) number of G's = 25,837,735 bp (21.93%) number of N's = 226,613 bp (0.19%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,064,189 number of insertions = 9,832 mapped reads with insertion percentage = 0.54% number of deletions = 43,312 mapped reads with deletion percentage = 2.37% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3495X There is a 3.3% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10403204 0.04173792610129545 0.6267790091039853 chr2 243199373 12313325 0.050630578722750244 0.4160747816965299 chr3 198022430 9554999 0.04825210457219417 0.2462026026840076 chr4 191154276 5899355 0.030861747502839015 0.21131079016260165 chr5 180915260 7160747 0.039580668872266495 0.22294815254281078 chr6 171115067 6793986 0.039704195072430414 0.25323784765570884 chr7 159138663 6838937 0.04297470439348859 0.42131997495241275 chr8 146364022 6185318 0.042259825300509986 0.6632670466747675 chr9 141213431 4300978 0.030457287026755975 0.26434512690231915 chr10 135534747 5350056 0.0394736856667464 0.30344950701928086 chr11 135006516 4791864 0.03549357573230021 0.2595871900754666 chr12 133851895 6338119 0.04735173155374453 0.2459217969579683 chr13 115169878 3515977 0.030528616171669472 0.19688614051604625 chr14 107349540 3129011 0.029147875249395574 0.2012805033259287 chr15 102531392 3195260 0.03116372398416282 0.19835542539520346 chr16 90354753 2204899 0.02440268969580383 0.19446387184297848 chr17 81195210 3463136 0.04265197417433861 0.250321426693279 chr18 78077248 2868521 0.03673952493817405 0.4642057086964431 chr19 59128983 1721077 0.02910716390978685 0.41077036326040256 chr20 63025520 1811923 0.028749036898069225 0.19676829746065727 chr21 48129895 1619996 0.03365883096150532 0.21686061071554616 chr22 51304566 1106913 0.021575331131346086 0.16274971080646158 chrMT 16571 43032 2.596825779977068 2.2650066773085054 chrX 155270560 6925578 0.04460329118411114 0.2531965065600134 chrY 59373566 343125 0.005779086942495588 0.11897940868230902