BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472387.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 21,570,732 number of mapped reads = 21,399,563 (99.21%) number of supplementary alignments = 83,775 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,731,433 number of mapped paired reads (second in pair) = 10,668,130 number of mapped paired reads (both in pair) = 21,297,010 number of mapped paired reads (singletons) = 102,553 number of mapped bases = 2,102,841,509 bp number of sequenced bases = 2,102,566,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,935,906 duplication rate = 48.29% >>>>>>> Insert size mean insert size = 17,679.8825 std insert size = 1,293,650.2683 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 55.1487 >>>>>>> ACTG content number of A's = 566,633,673 bp (26.95%) number of C's = 485,696,234 bp (23.1%) number of T's = 567,872,638 bp (27.01%) number of G's = 482,103,305 bp (22.93%) number of N's = 260,450 bp (0.01%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 11,414,503 number of insertions = 118,950 mapped reads with insertion percentage = 0.55% number of deletions = 104,484 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.6793X std coverageData = 21.2935X There is a 5.55% of reference with a coverageData >= 1X There is a 2.39% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 280161364 1.1240147080716802 31.986487991515503 chr2 243199373 168693126 0.6936412866492053 21.62060470480691 chr3 198022430 179464634 0.9062843739469312 20.691930234665403 chr4 191154276 78559318 0.4109733752437743 16.297776805001014 chr5 180915260 111658857 0.6171887158662017 22.613411786924214 chr6 171115067 147385136 0.8613217911430324 20.332000035595673 chr7 159138663 114239732 0.7178628363869062 26.76885507433436 chr8 146364022 102177533 0.6981055289666747 17.87769776773008 chr9 141213431 89719584 0.6353473842017194 15.892708090594487 chr10 135534747 68649391 0.5065076854424644 20.099048094518214 chr11 135006516 82459402 0.6107809048268455 18.137050046686042 chr12 133851895 91375200 0.6826589941068821 17.750595589969077 chr13 115169878 31472207 0.27326769417954927 8.162178788149578 chr14 107349540 49148297 0.4578342580694803 13.929356721384694 chr15 102531392 44599793 0.43498671119182697 13.402437169903454 chr16 90354753 112328495 1.2431940907414134 37.23918272684339 chr17 81195210 98452939 1.2125461465029772 32.384783319185445 chr18 78077248 30355186 0.38878401554317077 16.321431267222923 chr19 59128983 57464284 0.971846310970713 21.70478055975442 chr20 63025520 50453667 0.8005275799390469 20.442758415247763 chr21 48129895 14327648 0.297687082010048 14.414052183558953 chr22 51304566 23660449 0.4611762820486582 15.403225580220084 chrMT 16571 2330 0.14060708466598273 0.41793027019272305 chrX 155270560 73188864 0.4713634316769386 16.68483870187524 chrY 59373566 2844073 0.04790133373494865 2.3027420583461273