BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008777.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 = 2,733,547 number of mapped reads = 2,534,302 (92.71%) number of supplementary alignments = 15,227 (0.56%) number of secondary alignments = 0 number of mapped bases = 170,145,082 bp number of sequenced bases = 170,066,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,399 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4063 >>>>>>> ACTG content number of A's = 46,154,286 bp (27.14%) number of C's = 32,636,120 bp (19.19%) number of T's = 52,219,641 bp (30.71%) number of G's = 38,817,914 bp (22.83%) number of N's = 238,852 bp (0.14%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,398,985 number of insertions = 12,415 mapped reads with insertion percentage = 0.49% number of deletions = 44,422 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.055X std coverageData = 0.522X There is a 4.65% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% 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 13734104 0.055101583879303556 1.06207023545297 chr2 243199373 16330029 0.06714667393488716 0.6941605336905544 chr3 198022430 12179623 0.06150627986940671 0.29119808042412715 chr4 191154276 10481874 0.0548346300137173 0.2835271564845524 chr5 180915260 9228474 0.05100992586252812 0.25738539620589124 chr6 171115067 8451265 0.04938936791580136 0.308754906966871 chr7 159138663 8604290 0.054067879155174255 0.7888506214644743 chr8 146364022 11349821 0.07754515655493534 0.6764381319447262 chr9 141213431 6587631 0.046650173098619775 0.37816503304540466 chr10 135534747 8317947 0.06137132494887086 0.5329975747917279 chr11 135006516 7856046 0.05819012468998163 0.3932799391030518 chr12 133851895 7310095 0.05461330973311958 0.27135292853598525 chr13 115169878 4882266 0.04239186569252075 0.2355846121072178 chr14 107349540 4997664 0.046555057432011354 0.27436891628986304 chr15 102531392 4051802 0.039517672792348316 0.22848542018379592 chr16 90354753 4534443 0.05018488623393171 0.31745967723097046 chr17 81195210 5018405 0.06180666322557698 0.3215945519113899 chr18 78077248 4186532 0.05362038375123058 0.6408236260129812 chr19 59128983 3586864 0.06066168937828679 0.7239872604771537 chr20 63025520 4175089 0.06624441972077343 0.30407532222138156 chr21 48129895 2066931 0.042944847479929056 0.2583558497678333 chr22 51304566 2041953 0.0398006095597807 0.22775818002111248 chrMT 16571 42327 2.5542815762476616 2.1720831773682256 chrX 155270560 9704295 0.062499259357343726 0.3134900876177697 chrY 59373566 425312 0.0071633224792325935 0.15652353873254965