BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,309,364 number of mapped reads = 22,720,781 (97.47%) number of supplementary alignments = 503,308 (2.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,412,690 number of mapped paired reads (second in pair) = 11,308,091 number of mapped paired reads (both in pair) = 22,379,570 number of mapped paired reads (singletons) = 341,211 number of mapped bases = 2,084,152,789 bp number of sequenced bases = 2,082,701,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,598,814 duplication rate = 5.49% >>>>>>> Insert size mean insert size = 230,753.2823 std insert size = 4,700,814.9796 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 52.7739 >>>>>>> ACTG content number of A's = 591,472,270 bp (28.4%) number of C's = 413,040,594 bp (19.83%) number of T's = 602,520,302 bp (28.93%) number of G's = 475,358,436 bp (22.82%) number of N's = 310,348 bp (0.01%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 21,270,642 number of insertions = 336,217 mapped reads with insertion percentage = 1.45% number of deletions = 991,722 mapped reads with deletion percentage = 4.26% homopolymer indels = 51.65% >>>>>>> Coverage mean coverageData = 0.6732X std coverageData = 2.8335X There is a 32.05% of reference with a coverageData >= 1X There is a 15.72% of reference with a coverageData >= 2X There is a 7.88% of reference with a coverageData >= 3X There is a 4.29% of reference with a coverageData >= 4X There is a 2.43% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 170153416 0.68265994811704 3.9466779451462997 chr2 243199373 182761559 0.7514886109513119 4.585128444710869 chr3 198022430 141526847 0.714701092194455 1.409735843766422 chr4 191154276 126608268 0.6623355263054644 2.1402640758258293 chr5 180915260 126213046 0.6976362635191746 1.367041103529271 chr6 171115067 120402641 0.7036355308209066 1.4642425224622475 chr7 159138663 107786039 0.677308939060271 2.0512780899441276 chr8 146364022 106643406 0.7286176243503338 1.771722388923691 chr9 141213431 91171555 0.6456294869005768 3.4092809134452176 chr10 135534747 104109799 0.7681410214312054 6.615475599569355 chr11 135006516 97089809 0.7191490594424346 2.1321208735470365 chr12 133851895 93682383 0.6998958288935693 1.3870406755182285 chr13 115169878 62706805 0.5444722707789966 1.2006040424376876 chr14 107349540 62758404 0.5846173537399415 1.3149962983850272 chr15 102531392 61607689 0.6008666009333025 1.330159155726969 chr16 90354753 65173255 0.7213041133541697 3.601839659782171 chr17 81195210 54106691 0.666377868842263 1.9352763129053228 chr18 78077248 55835594 0.7151327106201284 3.46180466880301 chr19 59128983 34080679 0.5763785756301609 2.3055264323197155 chr20 63025520 48170533 0.7643020319388083 1.574772263748915 chr21 48129895 26926058 0.5594456002864747 1.8251989003474511 chr22 51304566 25518506 0.4973924932919226 1.2576807014514766 chrMT 16571 186959 11.282300404320802 6.059628875994713 chrX 155270560 114463962 0.7371903727274507 1.6654809528410863 chrY 59373566 4468886 0.07526726624437549 1.7805845842787582