BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240067.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 = 1,664,120 number of mapped reads = 1,427,339 (85.77%) number of supplementary alignments = 10,480 (0.63%) number of secondary alignments = 0 number of mapped bases = 94,728,182 bp number of sequenced bases = 94,693,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,304 duplication rate = 8.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5114 >>>>>>> ACTG content number of A's = 26,495,644 bp (27.98%) number of C's = 16,831,681 bp (17.77%) number of T's = 30,980,233 bp (32.72%) number of G's = 20,377,645 bp (21.52%) number of N's = 8,548 bp (0.01%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 769,746 number of insertions = 6,910 mapped reads with insertion percentage = 0.48% number of deletions = 20,208 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.4934X There is a 2.07% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.19% 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 5950182 0.023872285557916425 0.7158975689423696 chr2 243199373 6986447 0.028727241003207685 0.4588090782764409 chr3 198022430 5378571 0.027161423077173633 0.22634042228236217 chr4 191154276 7762599 0.04060907850159732 0.28967214608068564 chr5 180915260 9836605 0.054371339377341635 0.321711348934182 chr6 171115067 5467118 0.0319499509648674 0.3251159005662883 chr7 159138663 7232461 0.045447541556887405 0.7126095973794178 chr8 146364022 5326359 0.036391176787967744 1.32723571751983 chr9 141213431 3802307 0.026925958622165336 0.41923401586871023 chr10 135534747 3909654 0.028846137883741355 0.37850542211235016 chr11 135006516 4184596 0.030995511357392556 0.33420399801527156 chr12 133851895 5090419 0.038030234835300616 0.2858492020228546 chr13 115169878 1561876 0.013561497390836865 0.16033006056471097 chr14 107349540 3358924 0.03128959844634639 0.2730543357354701 chr15 102531392 1562071 0.015235051134388188 0.17348558478069162 chr16 90354753 2297782 0.025430671035092087 0.23590594564682546 chr17 81195210 1601795 0.01972770314899118 0.20209943710692135 chr18 78077248 3585032 0.04591647492493588 0.7427554643106835 chr19 59128983 1478293 0.025001157215912204 0.5430486399172828 chr20 63025520 2250564 0.035708773208059215 0.2754177184549688 chr21 48129895 920271 0.019120569450650163 0.20850054053527714 chr22 51304566 623658 0.012155994068832002 0.1433320175386845 chrMT 16571 12411 0.7489590248023655 1.2068429621404924 chrX 155270560 4316186 0.027797838817609725 0.2627085510300039 chrY 59373566 232001 0.003907479634960784 0.1161540263007313