BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008797.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 = 1,270,993 number of mapped reads = 1,141,487 (89.81%) number of supplementary alignments = 7,418 (0.58%) number of secondary alignments = 0 number of mapped bases = 76,205,638 bp number of sequenced bases = 76,164,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,624 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8336 >>>>>>> ACTG content number of A's = 21,356,787 bp (28.04%) number of C's = 14,130,294 bp (18.55%) number of T's = 23,480,511 bp (30.83%) number of G's = 17,171,117 bp (22.54%) number of N's = 26,269 bp (0.03%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 665,325 number of insertions = 6,107 mapped reads with insertion percentage = 0.53% number of deletions = 23,200 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.3765X There is a 2.23% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 6789090 0.02723800635987182 0.8382032956234637 chr2 243199373 6987773 0.02873269331989602 0.4196070966739999 chr3 198022430 5962229 0.030108856860306177 0.2074842620739114 chr4 191154276 3989247 0.020869253272681174 0.16786584807033633 chr5 180915260 3621822 0.020019438935112495 0.152806401958381 chr6 171115067 3913977 0.022873362753029806 0.18907740359277225 chr7 159138663 4221025 0.026524195443315995 0.43549732562295795 chr8 146364022 5854149 0.039997185920457964 0.38960307020719287 chr9 141213431 2380837 0.01685984812591941 0.3190955453396588 chr10 135534747 4352118 0.03211071770399955 0.5375586641500447 chr11 135006516 3197531 0.02368427165396965 0.30242745108720265 chr12 133851895 3370385 0.025179957295337507 0.17253011444655617 chr13 115169878 1776293 0.01542324287258514 0.12896690024561006 chr14 107349540 2277410 0.021214902271588683 0.1677430683516449 chr15 102531392 1997831 0.019485066583315284 0.14967409098276863 chr16 90354753 2146892 0.023760698012200862 0.23403471429983877 chr17 81195210 2150999 0.026491698217173155 0.22591993996688242 chr18 78077248 1483259 0.01899732685250382 0.6127951538242513 chr19 59128983 1665406 0.028165645940502648 0.5141237251030103 chr20 63025520 1739860 0.027605642920518546 0.1852446383867286 chr21 48129895 796413 0.016547158476036567 0.1550892699634293 chr22 51304566 935629 0.01823675888808805 0.14290800393772846 chrMT 16571 7381 0.44541669181099514 0.7077375122116215 chrX 155270560 4338753 0.027943178668254947 0.21631011256659657 chrY 59373566 249329 0.004199326683527817 0.14266558154348077