BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240221.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 = 2,037,820 number of mapped reads = 1,473,995 (72.33%) number of supplementary alignments = 15,107 (0.74%) number of secondary alignments = 0 number of mapped bases = 97,100,853 bp number of sequenced bases = 97,051,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 266,946 duplication rate = 12.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5808 >>>>>>> ACTG content number of A's = 27,325,063 bp (28.16%) number of C's = 17,402,807 bp (17.93%) number of T's = 31,598,916 bp (32.56%) number of G's = 20,715,913 bp (21.35%) number of N's = 8,972 bp (0.01%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 819,928 number of insertions = 7,167 mapped reads with insertion percentage = 0.48% number of deletions = 28,292 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.4901X There is a 1.18% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 6817195 0.027350764353762633 0.535997137956034 chr2 243199373 9434544 0.038793455277534784 0.5071349142331834 chr3 198022430 5534170 0.027947187598899782 0.3673227165804519 chr4 191154276 8811222 0.046094820290601295 0.4672291114051061 chr5 180915260 4864728 0.026889539334603394 0.36539993656286623 chr6 171115067 6341852 0.03706191460042499 0.5440192930361725 chr7 159138663 4993738 0.03137979109451234 0.4776119977370672 chr8 146364022 4182025 0.02857276633187902 1.0915020546505756 chr9 141213431 5647980 0.03999605391642952 0.47394827429290104 chr10 135534747 7018446 0.05178337035594274 0.5098821475272963 chr11 135006516 3619675 0.02681111332433762 0.40012826713691985 chr12 133851895 3498785 0.026139226493580834 0.35355012818261206 chr13 115169878 2942466 0.025548920004933928 0.3466223575029675 chr14 107349540 2687508 0.02503511426318175 0.356576731780039 chr15 102531392 2262045 0.022061974931540967 0.31225294927290526 chr16 90354753 3211501 0.035543243640984774 0.39711875687804243 chr17 81195210 2487163 0.03063189318680252 0.3889931705282274 chr18 78077248 2330243 0.02984535264357678 0.6638507091608209 chr19 59128983 1290910 0.021832102202738714 0.3744004190549873 chr20 63025520 1800045 0.028560573558139624 0.3600208132408565 chr21 48129895 1194678 0.02482195317484071 0.3453733723967868 chr22 51304566 1791877 0.03492626757626212 0.3750859878035192 chrMT 16571 72029 4.346690000603464 5.520358941364528 chrX 155270560 3996220 0.02573713909449415 0.36087638006415884 chrY 59373566 269808 0.0045442444875216014 0.1308556397208813