BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004012.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,083,252 number of mapped reads = 2,757,149 (89.42%) number of supplementary alignments = 25,993 (0.84%) number of secondary alignments = 0 number of mapped bases = 183,901,636 bp number of sequenced bases = 183,832,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,577 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9673 >>>>>>> ACTG content number of A's = 51,294,580 bp (27.9%) number of C's = 35,101,304 bp (19.09%) number of T's = 56,912,403 bp (30.96%) number of G's = 40,492,905 bp (22.03%) number of N's = 31,132 bp (0.02%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,573,021 number of insertions = 12,734 mapped reads with insertion percentage = 0.46% number of deletions = 40,348 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0594X std coverageData = 0.4695X There is a 4.73% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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 13638867 0.05471949054843077 0.8578805516267602 chr2 243199373 12588064 0.05176026502338063 0.5046658523406207 chr3 198022430 11543402 0.05829340645905618 0.2893190419837202 chr4 191154276 12853615 0.06724210030227103 0.3306742877997679 chr5 180915260 11659630 0.06444801837058964 0.3061152562670689 chr6 171115067 11226640 0.06560871696938295 0.3414150434149501 chr7 159138663 11239216 0.07062530115638838 0.7264928115526456 chr8 146364022 13732872 0.09382682856310139 0.622078174945746 chr9 141213431 7372230 0.05220629473976877 0.4097716114396945 chr10 135534747 7752763 0.057201294661360896 0.40087834159539837 chr11 135006516 6625455 0.04907507575412138 0.3625683562387717 chr12 133851895 8795478 0.06571052281329301 0.31572231525533434 chr13 115169878 6012032 0.052201427182201235 0.29005006150437573 chr14 107349540 4672282 0.04352400578521343 0.2820223853036356 chr15 102531392 5968596 0.058212376556830515 0.2939922684913921 chr16 90354753 5172276 0.05724409428688273 0.31270164486938146 chr17 81195210 4166447 0.051313950662853144 0.29555968660857423 chr18 78077248 5399211 0.06915216837560668 0.7525874347102877 chr19 59128983 2908800 0.049194149001345076 0.6071429971601882 chr20 63025520 4084202 0.06480235307856246 0.32368640279963057 chr21 48129895 2438554 0.05066609848203492 0.2909831331327723 chr22 51304566 1540473 0.030026040957056337 0.20286294825547335 chrMT 16571 25054 1.5119184116830608 1.619659157579586 chrX 155270560 12034902 0.07750923291575686 0.3739541414348349 chrY 59373566 450575 0.007588814860808596 0.13900098730256824