BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084906.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 = 2,201,872 number of mapped reads = 1,980,187 (89.93%) number of supplementary alignments = 15,932 (0.72%) number of secondary alignments = 0 number of mapped bases = 135,189,756 bp number of sequenced bases = 135,138,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,124 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3308 >>>>>>> ACTG content number of A's = 38,825,961 bp (28.73%) number of C's = 24,548,229 bp (18.17%) number of T's = 43,459,600 bp (32.16%) number of G's = 28,283,889 bp (20.93%) number of N's = 20,875 bp (0.02%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,105,263 number of insertions = 10,231 mapped reads with insertion percentage = 0.51% number of deletions = 29,031 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0437X std coverageData = 0.3497X There is a 3.7% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% 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% 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 10169738 0.04080125441292281 0.5779651460232187 chr2 243199373 12169239 0.0500381183137343 0.37107655709806286 chr3 198022430 9565378 0.04830451782659166 0.2507442155567566 chr4 191154276 8376523 0.04382074612864009 0.24058981043087735 chr5 180915260 7979496 0.044106262788445816 0.24315677197736169 chr6 171115067 9863500 0.057642498541639234 0.2874828269308607 chr7 159138663 8088171 0.050824676087670786 0.3227510328430457 chr8 146364022 6925338 0.04731584924606677 0.7152033837291614 chr9 141213431 7271824 0.05149527172100223 0.34870719371142445 chr10 135534747 4297953 0.031711078488234457 0.24391409530541858 chr11 135006516 5939575 0.04399472837296239 0.27175193039259804 chr12 133851895 5948515 0.044441021922028076 0.24380723664835985 chr13 115169878 4234083 0.03676380554991992 0.21709663386436018 chr14 107349540 2731420 0.025444170510651468 0.19394969584430868 chr15 102531392 3439114 0.03354205900179332 0.20819215460531504 chr16 90354753 2530849 0.028010136887873512 0.20911416448291148 chr17 81195210 3263101 0.04018834362273341 0.23167833697238546 chr18 78077248 4552335 0.05830552583000876 0.5637487507875197 chr19 59128983 2618732 0.04428846679131958 0.3859559324684878 chr20 63025520 2587644 0.041057082908637646 0.24273915997873582 chr21 48129895 1323136 0.02749093884372696 0.19945481425447464 chr22 51304566 1252181 0.024406814005599423 0.17508538481291722 chrMT 16571 81781 4.935187978999457 3.445834375031227 chrX 155270560 9670955 0.06228453739073267 0.29864029509132733 chrY 59373566 309175 0.00520728365885923 0.13129792746735336