BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082325.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,849,002 number of mapped reads = 2,559,364 (89.83%) number of supplementary alignments = 26,625 (0.93%) number of secondary alignments = 0 number of mapped bases = 173,496,928 bp number of sequenced bases = 173,436,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,739 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9557 >>>>>>> ACTG content number of A's = 48,928,310 bp (28.21%) number of C's = 32,469,780 bp (18.72%) number of T's = 54,262,450 bp (31.29%) number of G's = 37,772,329 bp (21.78%) number of N's = 3,410 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,438,119 number of insertions = 13,370 mapped reads with insertion percentage = 0.52% number of deletions = 37,500 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.4846X There is a 4.79% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13733989 0.05510112249630062 0.8878031613629073 chr2 243199373 14917983 0.061340548768602295 0.552354052019501 chr3 198022430 11691135 0.059039448207963106 0.2736554129915703 chr4 191154276 11647614 0.06093305493202778 0.28946777573615745 chr5 180915260 11023310 0.06093079157612243 0.2811435509280277 chr6 171115067 10370953 0.060608064396807326 0.3349019080257509 chr7 159138663 9606311 0.0603644068569308 0.5964247967201718 chr8 146364022 8958733 0.06120857351132371 0.8890674618990272 chr9 141213431 7333482 0.05193190157669918 0.4340103959375654 chr10 135534747 8126998 0.0599624685173906 0.418123901305413 chr11 135006516 7862108 0.05823502622643784 0.402833048826199 chr12 133851895 7864960 0.0587586750266031 0.2807801157151913 chr13 115169878 5664562 0.049184405665516115 0.24896996613472003 chr14 107349540 5220948 0.04863502908349677 0.27529191039504614 chr15 102531392 4856058 0.047361670462837374 0.249982938470886 chr16 90354753 4626186 0.05120025063872401 0.28210391836065857 chr17 81195210 4270324 0.05259329953084671 0.29113233231019886 chr18 78077248 4728484 0.06056161200763634 0.7797413095217136 chr19 59128983 3090053 0.05225953235150349 0.6520541056278915 chr20 63025520 3420583 0.054272983388316355 0.2705551852795016 chr21 48129895 2238347 0.0465063761306772 0.26135971853326645 chr22 51304566 1752830 0.03416518521957675 0.20576961007000752 chrMT 16571 7474 0.4510289059199807 0.811733326572944 chrX 155270560 10060520 0.06479348048979794 0.33030945104076564 chrY 59373566 422983 0.007124096268699778 0.1519026939742005