BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234134.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 = 1,501,087 number of mapped reads = 717,044 (47.77%) number of supplementary alignments = 2,498 (0.17%) number of secondary alignments = 0 number of mapped bases = 41,980,561 bp number of sequenced bases = 41,950,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,259 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9942 >>>>>>> ACTG content number of A's = 10,986,372 bp (26.19%) number of C's = 6,410,700 bp (15.28%) number of T's = 14,136,556 bp (33.7%) number of G's = 10,410,837 bp (24.82%) number of N's = 6,200 bp (0.01%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 467,763 number of insertions = 3,700 mapped reads with insertion percentage = 0.51% number of deletions = 16,955 mapped reads with deletion percentage = 2.33% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1712X There is a 1.14% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 3637136 0.014592284606584792 0.19238604039827137 chr2 243199373 2962133 0.012179854591977094 0.1667826979406533 chr3 198022430 3590265 0.018130597629773558 0.16639991869649795 chr4 191154276 2153480 0.011265664807833019 0.13155564677786502 chr5 180915260 2520474 0.013931793260557457 0.1430768191301606 chr6 171115067 2795341 0.016336030771621064 0.17445252966049413 chr7 159138663 2554944 0.01605482886330395 0.19480837205013898 chr8 146364022 2119840 0.014483340721533329 0.30143759585405855 chr9 141213431 1684932 0.011931811217022267 0.15705019887113641 chr10 135534747 2043171 0.01507488703247441 0.16446820908253584 chr11 135006516 1974960 0.014628627258257669 0.18712844946782686 chr12 133851895 1621302 0.012112656305687716 0.1305129055848897 chr13 115169878 1617903 0.01404797007773161 0.14642670274589165 chr14 107349540 1745492 0.016259892683284902 0.15599039038243726 chr15 102531392 947938 0.009245344099102838 0.11656953254175101 chr16 90354753 1062200 0.011755884054046388 0.13319276457670515 chr17 81195210 1007322 0.012406175191861688 0.13448935035093593 chr18 78077248 990574 0.012687101881459757 0.27482119216730694 chr19 59128983 936995 0.01584662804026242 0.1632750493751718 chr20 63025520 953625 0.015130775596932797 0.16071987887047576 chr21 48129895 662578 0.013766454300388564 0.14152963145838487 chr22 51304566 372783 0.007266078422727521 0.10050274414574592 chrMT 16571 31357 1.8922816969404381 2.4355569336556977 chrX 155270560 1834565 0.011815279084457479 0.1382007325318594 chrY 59373566 159251 0.002682186884311446 0.06500806527087398