BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524447.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 5,707,892 number of mapped reads = 5,260,823 (92.17%) number of supplementary alignments = 12,102 (0.21%) number of secondary alignments = 0 number of mapped bases = 306,532,346 bp number of sequenced bases = 306,435,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 586,999 duplication rate = 8.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4702 >>>>>>> ACTG content number of A's = 78,396,268 bp (25.58%) number of C's = 51,598,346 bp (16.84%) number of T's = 98,512,680 bp (32.15%) number of G's = 77,922,198 bp (25.43%) number of N's = 6,117 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,426,830 number of insertions = 20,487 mapped reads with insertion percentage = 0.39% number of deletions = 56,845 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.099X std coverageData = 0.7928X There is a 7.03% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 29773367 0.11945152585998974 1.609989797687509 chr2 243199373 24241486 0.09967741980979532 0.9001901669569037 chr3 198022430 18583961 0.09384775754948568 0.4216741877621974 chr4 191154276 17349521 0.09076187759461891 0.5270009947078789 chr5 180915260 16480265 0.09109383586547647 0.41122236498679166 chr6 171115067 13121361 0.07668150578464257 0.5830672125972663 chr7 159138663 15101982 0.09489825863373001 1.0595589945690382 chr8 146364022 28197657 0.1926542917767045 0.7931938444612081 chr9 141213431 12983695 0.09194376843658732 0.6560089063898782 chr10 135534747 15895706 0.11728140828713098 0.7888863868673991 chr11 135006516 10564689 0.07825317853547158 0.7756646087231303 chr12 133851895 14164504 0.10582221491895949 0.44351587735999554 chr13 115169878 6909187 0.05999126785564538 0.33802199475948247 chr14 107349540 7190079 0.06697820037235372 0.3662051788999189 chr15 102531392 8051231 0.07852454592638321 0.4173340526614828 chr16 90354753 9465867 0.10476335428640926 0.49987686675130794 chr17 81195210 10577781 0.13027592391226034 0.5446866308922629 chr18 78077248 7285871 0.09331618604180311 1.3343481299337367 chr19 59128983 6207110 0.1049757612100313 1.093852496303029 chr20 63025520 8740713 0.1386852976381631 0.5184815739928643 chr21 48129895 4166389 0.08656551193390304 0.4749797639963996 chr22 51304566 2492899 0.048590197605413915 0.29591088086798706 chrMT 16571 163946 9.89354897109408 6.796226014181213 chrX 155270560 17829582 0.11482912150249217 0.5804896703491642 chrY 59373566 993497 0.016732985180644193 0.4257207357418034