BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716984.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 = 3,335,013 number of mapped reads = 3,070,979 (92.08%) number of supplementary alignments = 18,766 (0.56%) number of secondary alignments = 0 number of mapped bases = 180,249,242 bp number of sequenced bases = 180,196,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,397 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6672 >>>>>>> ACTG content number of A's = 44,972,569 bp (24.96%) number of C's = 35,005,233 bp (19.43%) number of T's = 56,466,843 bp (31.34%) number of G's = 43,749,901 bp (24.28%) number of N's = 2,219 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 891,202 number of insertions = 11,948 mapped reads with insertion percentage = 0.39% number of deletions = 32,964 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.4484X There is a 4.8% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13274194 0.05325641294991999 0.6912489807344816 chr2 243199373 18322950 0.07534127154184728 0.6360539995612453 chr3 198022430 11973730 0.060466534018393775 0.29744176229522834 chr4 191154276 9817960 0.05136144587212896 0.32034840922179725 chr5 180915260 9434945 0.05215118392997915 0.2678850663760717 chr6 171115067 9701962 0.05669846711978905 0.3113391692725234 chr7 159138663 8821047 0.05542994287943716 0.6676990711201849 chr8 146364022 17042157 0.11643679072989672 0.6185399297659928 chr9 141213431 7369358 0.05218595673098545 0.3381253837687313 chr10 135534747 8461567 0.062430979415190116 0.5935018519412002 chr11 135006516 6087540 0.045090712510498385 0.34393909138579976 chr12 133851895 8260633 0.06171472581691877 0.3167214749002256 chr13 115169878 4766610 0.04138764477982689 0.23687590225704822 chr14 107349540 5910767 0.05506094390343918 0.28576879785989207 chr15 102531392 4312189 0.04205725598653728 0.25024510946337825 chr16 90354753 5522128 0.061116076538884456 0.30940780324748623 chr17 81195210 7849305 0.09667202043076187 0.39486436287299476 chr18 78077248 4235338 0.05424548262766638 0.5582002020727002 chr19 59128983 3599775 0.06088004253345605 0.5960000691420889 chr20 63025520 4106928 0.06516293717211695 0.3203268528774831 chr21 48129895 1850409 0.03844614662051517 0.2616309123658973 chr22 51304566 2855081 0.05564964724582214 0.27693711604254956 chrMT 16571 87047 5.252972059622231 3.8016937724694313 chrX 155270560 6156173 0.03964803759321793 0.27926857090328483 chrY 59373566 429449 0.007232999951527251 0.18651686831468084