BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708533.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 20,993,248 number of mapped reads = 20,519,507 (97.74%) number of supplementary alignments = 553 (0%) number of secondary alignments = 0 number of mapped bases = 1,023,563,310 bp number of sequenced bases = 1,023,474,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,344 duplication rate = 1.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4005 >>>>>>> ACTG content number of A's = 315,248,597 bp (30.8%) number of C's = 194,988,537 bp (19.05%) number of T's = 315,241,977 bp (30.8%) number of G's = 197,959,306 bp (19.34%) number of N's = 35,691 bp (0%) GC percentage = 38.39% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 1,930,073 number of insertions = 58,521 mapped reads with insertion percentage = 0.28% number of deletions = 53,534 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.78% >>>>>>> Coverage mean coverageData = 0.3306X std coverageData = 0.6785X There is a 24.41% of reference with a coverageData >= 1X There is a 6.37% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.04% 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 79231730 0.3178797696957393 0.6776719946988601 chr2 243199373 98286838 0.40414100080759663 0.7414490227012479 chr3 198022430 72731525 0.3672893267696998 0.6982944071815227 chr4 191154276 90663235 0.4742935229971 0.799310158491209 chr5 180915260 75588131 0.41780959218144453 0.7481358202344087 chr6 171115067 62681000 0.3663090638301302 0.7081955851260742 chr7 159138663 63017681 0.3959922737317455 0.7412110588484887 chr8 146364022 55416147 0.37861864031038994 0.709719001698901 chr9 141213431 41392931 0.29312318741125976 0.6452462014173164 chr10 135534747 38785638 0.28616748736764896 0.6134997544047847 chr11 135006516 49981910 0.3702185011573812 0.7185217955725931 chr12 133851895 51201259 0.38252173418986707 0.730471566379909 chr13 115169878 41016163 0.3561362025581029 0.7013719810712774 chr14 107349540 33583086 0.31283865771572006 0.6632139895689781 chr15 102531392 28376258 0.2767567809866465 0.6290234918181079 chr16 90354753 17783021 0.19681334306785167 0.5177809494420887 chr17 81195210 17175185 0.21152953480876518 0.544361630765307 chr18 78077248 28537092 0.36549817944402957 0.6963216534845846 chr19 59128983 8384875 0.1418065147509809 0.4313153376943196 chr20 63025520 14887551 0.23621464765383926 0.5647253245000005 chr21 48129895 10553903 0.21927957665396944 0.5549323991537728 chr22 51304566 5632455 0.1097846729665348 0.38204104331076133 chrMT 16571 1242 0.07495021422967835 0.3112083428623237 chrX 155270560 34674549 0.22331695718750547 0.5422747023912755 chrY 59373566 3979905 0.06703159786629626 0.30265311778526227