BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085045.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 = 3,139,364 number of mapped reads = 2,893,368 (92.16%) number of supplementary alignments = 16,065 (0.51%) number of secondary alignments = 0 number of mapped bases = 196,010,574 bp number of sequenced bases = 195,933,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,670 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1092 >>>>>>> ACTG content number of A's = 56,342,665 bp (28.76%) number of C's = 37,649,124 bp (19.22%) number of T's = 59,955,545 bp (30.6%) number of G's = 41,964,533 bp (21.42%) number of N's = 22,052 bp (0.01%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,793,792 number of insertions = 13,708 mapped reads with insertion percentage = 0.47% number of deletions = 43,883 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.4803X There is a 5.33% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 17074208 0.06850216834565079 0.740709769313053 chr2 243199373 20077850 0.0825571618558408 0.5807566029214789 chr3 198022430 11962662 0.06041064136017319 0.2886942639866894 chr4 191154276 11095209 0.05804321635996257 0.28611550791870294 chr5 180915260 10118387 0.055928875209310704 0.2697113161575492 chr6 171115067 13695763 0.08003832298414727 0.48461113595542415 chr7 159138663 17514680 0.11005923808722712 0.6542438163879055 chr8 146364022 12075183 0.08250103293827223 0.812362085008089 chr9 141213431 6863846 0.048606183925946816 0.44591715193694004 chr10 135534747 13315877 0.09824696098041928 0.5815718483516528 chr11 135006516 6866210 0.050858360051303 0.4158032819810312 chr12 133851895 8084104 0.060395887559156335 0.28989641181202036 chr13 115169878 4003097 0.034758194325776745 0.20824093719371184 chr14 107349540 6400640 0.059624289028159784 0.305241141240421 chr15 102531392 3234261 0.03154410504833485 0.20670857044237714 chr16 90354753 5034441 0.05571860729894309 0.29489223912593454 chr17 81195210 3270898 0.0402843714549171 0.2747123984383866 chr18 78077248 4585544 0.05873086100575676 0.8605413281379516 chr19 59128983 3111175 0.052616751416137156 0.5102599402699024 chr20 63025520 4252170 0.06746743224014654 0.3039289515321381 chr21 48129895 2307243 0.04793783572559217 0.2756643439590932 chr22 51304566 1366059 0.02662646049866205 0.18214565268903404 chrMT 16571 8188 0.49411622714380543 0.772081688644003 chrX 155270560 9311197 0.05996756242780344 0.3252769148248834 chrY 59373566 381682 0.0064284836790837185 0.12948829636533982