BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004013.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 = 2,397,072 number of mapped reads = 2,076,308 (86.62%) number of supplementary alignments = 23,944 (1%) number of secondary alignments = 0 number of mapped bases = 137,997,838 bp number of sequenced bases = 137,938,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,043 duplication rate = 4.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6413 >>>>>>> ACTG content number of A's = 37,915,909 bp (27.49%) number of C's = 26,242,290 bp (19.02%) number of T's = 42,910,717 bp (31.11%) number of G's = 30,846,878 bp (22.36%) number of N's = 23,069 bp (0.02%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,226,720 number of insertions = 9,947 mapped reads with insertion percentage = 0.48% number of deletions = 33,944 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.83% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.3924X There is a 3.48% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 11183019 0.04486656424418698 0.6493112008401627 chr2 243199373 11157875 0.045879538513448385 0.43090612843024656 chr3 198022430 8553210 0.04319313726227882 0.2544189530748054 chr4 191154276 8047040 0.042097096483470764 0.2621385099795477 chr5 180915260 7349849 0.04062592066584101 0.24832482260212052 chr6 171115067 8009634 0.04680846719359903 0.2821564420781932 chr7 159138663 8928170 0.05610308539540765 0.5226977727937256 chr8 146364022 9139604 0.06244433485163451 0.5249324360695129 chr9 141213431 5638747 0.03993067061730127 0.333634769906422 chr10 135534747 6244661 0.04607424397228557 0.3513573895256477 chr11 135006516 5818744 0.04309972712724473 0.32770772110709623 chr12 133851895 5856383 0.04375270891756893 0.25832488907477164 chr13 115169878 4551827 0.03952272138379794 0.25435190883744696 chr14 107349540 3256246 0.030333115540131798 0.23546845211424564 chr15 102531392 4254069 0.04149040520195025 0.24759552146355115 chr16 90354753 4099908 0.04537567603112146 0.27910414607697226 chr17 81195210 3779829 0.04655236435745409 0.2824138511953557 chr18 78077248 4097131 0.05247535107794783 0.638075868829419 chr19 59128983 2383076 0.04030301011603734 0.4843490908916541 chr20 63025520 2993072 0.04748984220994924 0.28055082020333916 chr21 48129895 1681381 0.034934233702359 0.2386591744616266 chr22 51304566 1891249 0.03686317120390415 0.23203439974696455 chrMT 16571 603724 36.43256291110977 22.597031397322613 chrX 155270560 8143793 0.052449047649470705 0.3136378398053064 chrY 59373566 335597 0.0056522965118854405 0.11422819813856509