BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173993.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,838,304 number of mapped reads = 10,608,223 (97.88%) number of supplementary alignments = 1,490,850 (13.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,301,912 number of mapped paired reads (second in pair) = 5,306,311 number of mapped paired reads (both in pair) = 10,455,310 number of mapped paired reads (singletons) = 152,913 number of mapped bases = 1,208,852,188 bp number of sequenced bases = 1,208,021,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,659,007 duplication rate = 65.62% >>>>>>> Insert size mean insert size = 1,081,021.445 std insert size = 9,567,418.3159 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.4743 >>>>>>> ACTG content number of A's = 360,651,376 bp (29.85%) number of C's = 240,066,174 bp (19.87%) number of T's = 357,844,945 bp (29.62%) number of G's = 249,450,420 bp (20.65%) number of N's = 8,773 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 10,194,113 number of insertions = 133,946 mapped reads with insertion percentage = 1.21% number of deletions = 342,966 mapped reads with deletion percentage = 3.15% homopolymer indels = 41.2% >>>>>>> Coverage mean coverageData = 0.3905X std coverageData = 6.7093X There is a 7.98% of reference with a coverageData >= 1X There is a 6.1% of reference with a coverageData >= 2X There is a 4.64% of reference with a coverageData >= 3X There is a 3.77% of reference with a coverageData >= 4X There is a 2.87% of reference with a coverageData >= 5X There is a 2.38% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 1.04% of reference with a coverageData >= 10X There is a 0.79% of reference with a coverageData >= 11X There is a 0.72% of reference with a coverageData >= 12X There is a 0.54% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 97625082 0.391674378215491 3.0138286221716055 chr2 243199373 106020210 0.43593948739333305 22.128676493183555 chr3 198022430 80515486 0.4065978081371893 1.9369490084271375 chr4 191154276 80520528 0.42123320327921937 3.246355814494357 chr5 180915260 74792337 0.41341088087317784 1.9718406828260686 chr6 171115067 72291445 0.4224727037041104 2.4400433949846967 chr7 159138663 67653309 0.4251217631506682 3.109996474855015 chr8 146364022 61006212 0.41681153036365726 3.5450875060170612 chr9 141213431 51605743 0.3654450050151391 2.8996831996075505 chr10 135534747 61053519 0.45046396109773973 3.950160460944623 chr11 135006516 55366396 0.4101016576118445 2.0518657624398755 chr12 133851895 56330491 0.4208419387712068 2.0989573217539363 chr13 115169878 39526580 0.34320241270030694 1.7874031270847375 chr14 107349540 37762155 0.35176820506170775 1.8629985496029164 chr15 102531392 35660652 0.34780228088583837 1.8794285841040324 chr16 90354753 37483008 0.4148426812699051 2.743519611040377 chr17 81195210 33798738 0.4162651713075192 2.2988909781906424 chr18 78077248 33258470 0.4259687790225393 4.165140746097691 chr19 59128983 22928226 0.38776628375292704 2.4880859032490585 chr20 63025520 26301697 0.4173182069739369 2.155811317829544 chr21 48129895 17180941 0.35697025725902787 2.7279030852811794 chr22 51304566 15631493 0.30468034755425083 2.347658492886748 chrMT 16571 1074313 64.83090942007121 56.7934822303117 chrX 155270560 33950420 0.21865329783057394 1.444220528908748 chrY 59373566 9514737 0.1602520724458423 2.4525389627403955