BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472620.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 = 17,337,722 number of mapped reads = 17,188,372 (99.14%) number of supplementary alignments = 88,142 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,621,392 number of mapped paired reads (second in pair) = 8,566,980 number of mapped paired reads (both in pair) = 17,085,962 number of mapped paired reads (singletons) = 102,410 number of mapped bases = 1,695,993,083 bp number of sequenced bases = 1,695,777,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,656,255 duplication rate = 48.67% >>>>>>> Insert size mean insert size = 23,505.3484 std insert size = 1,539,626.5213 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 54.8064 >>>>>>> ACTG content number of A's = 459,038,833 bp (27.07%) number of C's = 391,048,601 bp (23.06%) number of T's = 460,057,166 bp (27.13%) number of G's = 385,322,601 bp (22.72%) number of N's = 310,397 bp (0.02%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,711,839 number of insertions = 99,679 mapped reads with insertion percentage = 0.57% number of deletions = 87,913 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 0.5479X std coverageData = 22.5909X There is a 3.68% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 276875166 1.1108303958849515 37.737340566950635 chr2 243199373 134358721 0.5524632705364746 21.679212872873666 chr3 198022430 124670832 0.6295793461377077 21.0176663370143 chr4 191154276 58824519 0.3077332102160247 18.01883601837779 chr5 180915260 70612016 0.3903043668068686 16.37442223271972 chr6 171115067 170123277 0.9942039586730256 37.203830298802025 chr7 159138663 66097174 0.41534327833331114 15.833246933542295 chr8 146364022 128603395 0.8786544209614573 33.062218470064714 chr9 141213431 72216766 0.5114015394187257 14.28641553856551 chr10 135534747 42790404 0.3157153788762375 11.954784277627972 chr11 135006516 64356354 0.47669072506100374 20.441489684323734 chr12 133851895 68525610 0.5119509888149136 20.14063071458065 chr13 115169878 45965703 0.39911219668045494 15.367490378542527 chr14 107349540 20263541 0.1887622527306591 6.595507914277301 chr15 102531392 20766630 0.20253923793407583 6.579314572886049 chr16 90354753 78312071 0.8667177807458563 31.889587886243547 chr17 81195210 50294245 0.619423793595706 15.714992322668444 chr18 78077248 6499455 0.08324390480566118 3.2727082909151384 chr19 59128983 48528103 0.8207160099472707 24.925939322720716 chr20 63025520 61315413 0.9728664356914469 32.928338737646115 chr21 48129895 8572316 0.17810793063230243 7.117460896173489 chr22 51304566 27303544 0.5321854588926841 24.79555463012621 chrMT 16571 4395 0.26522237644077 0.856605343618071 chrX 155270560 48371292 0.31152906256021745 13.498376639409393 chrY 59373566 1742141 0.029342030761635572 2.110223309103922