BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013161.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 = 3,608,378 number of mapped reads = 2,426,672 (67.25%) number of supplementary alignments = 20,159 (0.56%) number of secondary alignments = 0 number of mapped bases = 155,405,463 bp number of sequenced bases = 155,312,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,535 duplication rate = 8.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0794 >>>>>>> ACTG content number of A's = 41,892,340 bp (26.97%) number of C's = 28,344,078 bp (18.25%) number of T's = 49,375,930 bp (31.79%) number of G's = 35,457,633 bp (22.83%) number of N's = 242,989 bp (0.16%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,436,012 number of insertions = 10,291 mapped reads with insertion percentage = 0.42% number of deletions = 53,295 mapped reads with deletion percentage = 2.17% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.4875X There is a 3.27% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 11021663 0.044219199758784154 0.8707854344044296 chr2 243199373 13082614 0.05379378177919891 0.5754146855708334 chr3 198022430 11297999 0.05705413775601077 0.34542127321850846 chr4 191154276 9622751 0.05034023408401285 0.34788317232505034 chr5 180915260 9850676 0.05444911612210048 0.3345585035291642 chr6 171115067 8927574 0.052172927589129246 0.4132366680864229 chr7 159138663 9239918 0.05806205623331145 0.6188216567413 chr8 146364022 8784612 0.060018930061924644 0.46577497961431585 chr9 141213431 4790707 0.03392529284271834 0.36754962866711083 chr10 135534747 8222496 0.06066707012040241 0.5565836542910751 chr11 135006516 7643006 0.05661212678060665 0.41920510121968785 chr12 133851895 7604179 0.05681039480240455 0.34117776841732983 chr13 115169878 4085758 0.035475925397785 0.27142416628750354 chr14 107349540 4983676 0.04642475412563482 0.3191624043001352 chr15 102531392 4400486 0.042918426387891034 0.29616797121948174 chr16 90354753 3893922 0.04309592877753758 0.3170063463944629 chr17 81195210 3973117 0.04893289887420699 0.3554597374967787 chr18 78077248 4297770 0.05504510097487043 0.6646127879827594 chr19 59128983 2396712 0.040533624601661086 0.584083389040054 chr20 63025520 3233204 0.05129991787453717 0.33176739554593465 chr21 48129895 2805124 0.05828236276019302 0.3627755006188058 chr22 51304566 1386761 0.02702997234203287 0.23337504967071981 chrMT 16571 700121 42.24977370104399 19.83101791649039 chrX 155270560 8730303 0.05622638960019208 0.3585002629901122 chrY 59373566 430314 0.007247568724438751 0.18590365705120207