BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548931.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,478,495 number of mapped reads = 6,490,444 (86.79%) number of secondary alignments = 0 number of mapped bases = 256,709,152 bp number of sequenced bases = 256,681,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,701 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.986 >>>>>>> ACTG content number of A's = 75,060,029 bp (29.24%) number of C's = 53,129,180 bp (20.7%) number of T's = 75,487,746 bp (29.41%) number of G's = 53,002,034 bp (20.65%) number of N's = 2,219 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 734,386 number of insertions = 8,890 mapped reads with insertion percentage = 0.14% number of deletions = 21,239 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.0829X std coverageData = 0.9422X There is a 6.72% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20269959 0.08132360480658542 0.8723792700706096 chr2 243199373 21688330 0.08917921840201455 0.49381380747921827 chr3 198022430 17352144 0.08762716425608957 0.35117119068838226 chr4 191154276 16902822 0.08842502691386302 0.3670100721319551 chr5 180915260 15867154 0.0877048956511463 0.3555277048385256 chr6 171115067 14906302 0.0871127380033694 0.3849317467329431 chr7 159138663 14331062 0.09005392988629042 0.7365132587508848 chr8 146364022 13357217 0.0912602483689605 3.693346939149664 chr9 141213431 10739534 0.07605178858659697 0.4814592425583299 chr10 135534747 11808945 0.08712854276401903 0.45146785107151516 chr11 135006516 11572369 0.08571711457245515 0.5375800713338194 chr12 133851895 11707988 0.08746972166512847 0.3596722271246023 chr13 115169878 8412485 0.0730441426707077 0.31867637260085496 chr14 107349540 7901197 0.07360252312212982 0.37444570925269427 chr15 102531392 7381713 0.07199466286383784 0.31772742002685833 chr16 90354753 7056614 0.0780989794748263 0.35904449208321604 chr17 81195210 6675514 0.082215613457986 0.36267064825034906 chr18 78077248 6687653 0.08565431250855562 0.8381826069142767 chr19 59128983 5070916 0.08576024383845736 0.7814629092192911 chr20 63025520 5173888 0.08209195259317179 0.349501092757148 chr21 48129895 3295075 0.06846212733271079 0.3467740275847236 chr22 51304566 2837466 0.05530630548555854 0.33344158641682553 chrMT 16571 8820 0.5322551445295999 0.9133470162231937 chrX 155270560 14904695 0.09599176431127704 0.43197856603225165 chrY 59373566 799290 0.013462051445587755 0.18945910332678792