BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716930.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,639,988 number of mapped reads = 1,302,200 (79.4%) number of supplementary alignments = 6,972 (0.43%) number of secondary alignments = 0 number of mapped bases = 73,420,061 bp number of sequenced bases = 73,397,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,218 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1008 >>>>>>> ACTG content number of A's = 18,674,424 bp (25.44%) number of C's = 13,952,092 bp (19.01%) number of T's = 23,379,831 bp (31.85%) number of G's = 17,390,347 bp (23.69%) number of N's = 1,062 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 373,945 number of insertions = 5,924 mapped reads with insertion percentage = 0.45% number of deletions = 14,022 mapped reads with deletion percentage = 1.07% homopolymer indels = 38.74% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2416X There is a 2.16% of reference with a coverageData >= 1X There is a 0.15% 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% 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 5573112 0.02235947087168942 0.2675194752413976 chr2 243199373 6097950 0.025073872209366264 0.286448533003102 chr3 198022430 5745347 0.02901361729577806 0.1933447840164153 chr4 191154276 4403113 0.02303434216663822 0.1672493413049905 chr5 180915260 4022589 0.022234658369890966 0.15923027966378084 chr6 171115067 4339126 0.02535794232544116 0.1866992269529873 chr7 159138663 4778753 0.030028862313616397 0.573893828073792 chr8 146364022 5407970 0.03694876600207119 0.24591229743538523 chr9 141213431 3107964 0.022008982984061905 0.1812670747087564 chr10 135534747 3572943 0.026361822920582867 0.3074906319105655 chr11 135006516 2255839 0.016709112025378094 0.1703225140035493 chr12 133851895 3575577 0.026712935218436765 0.18564802120037516 chr13 115169878 2059816 0.017885023721219882 0.14282515612970953 chr14 107349540 1897317 0.017674197765542358 0.14599423272674242 chr15 102531392 1787073 0.01742952051211789 0.1449282575817392 chr16 90354753 2247693 0.024876311708804073 0.17867382915832689 chr17 81195210 3002276 0.03697602358562777 0.21306093069224144 chr18 78077248 1802329 0.023083920683269983 0.2688172291203333 chr19 59128983 1441271 0.024375034490276958 0.28085844752200084 chr20 63025520 1618180 0.025674996414150966 0.1775661582103811 chr21 48129895 712227 0.014798016908202273 0.13262305996963616 chr22 51304566 1006332 0.019614862349678585 0.15185629918136015 chrMT 16571 28304 1.7080441735562126 1.7065012879131474 chrX 155270560 2781542 0.017914162221093297 0.1646701474776423 chrY 59373566 155418 0.0026176295356758594 0.07039002858105647