BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716242.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 = 1,893,732 number of mapped reads = 1,738,596 (91.81%) number of supplementary alignments = 29,759 (1.57%) number of secondary alignments = 0 number of mapped bases = 136,314,135 bp number of sequenced bases = 136,253,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,623 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0182 >>>>>>> ACTG content number of A's = 34,810,911 bp (25.55%) number of C's = 26,455,684 bp (19.42%) number of T's = 42,446,551 bp (31.15%) number of G's = 32,531,891 bp (23.88%) number of N's = 8,213 bp (0.01%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,131,748 number of insertions = 13,147 mapped reads with insertion percentage = 0.75% number of deletions = 34,910 mapped reads with deletion percentage = 1.98% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.509X There is a 3.76% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 10936780 0.043878646946279826 0.8439752667583589 chr2 243199373 11644175 0.04787913248444107 0.7498807765806411 chr3 198022430 9046849 0.04568598112850145 0.24370953137406337 chr4 191154276 8742541 0.045735524116656434 0.26592749550714645 chr5 180915260 8072832 0.044622172833844974 0.24466937989643958 chr6 171115067 7860384 0.04593624709856789 0.31741990215830546 chr7 159138663 7578366 0.04762114911069725 0.6439561249770185 chr8 146364022 6961227 0.04756105294783441 0.6622276538467043 chr9 141213431 5829891 0.04128425291217519 0.5737560869580476 chr10 135534747 6441983 0.047530121556208754 0.4818088595986137 chr11 135006516 6149998 0.045553342032765294 0.48410561236869915 chr12 133851895 6165703 0.046063621288290314 0.2546306428661596 chr13 115169878 4287153 0.03722460312061805 0.21728674458169314 chr14 107349540 4107041 0.03825858033485751 0.3329208593488469 chr15 102531392 3883952 0.037880613188202884 0.22676566900085057 chr16 90354753 3941939 0.04362735627200486 0.28911301516900834 chr17 81195210 3709299 0.04568371705670815 0.2793897188334711 chr18 78077248 3832453 0.04908540065346566 1.102387770424412 chr19 59128983 2859205 0.04835538943735934 0.600843339925894 chr20 63025520 2720383 0.043163198018834274 0.26079454088477194 chr21 48129895 1754420 0.036451772853441713 0.2435028896188385 chr22 51304566 1492602 0.029092966111437333 0.19187902047103472 chrMT 16571 13628 0.8224005793253274 1.1783315957796427 chrX 155270560 7908902 0.050936262482726924 0.37859321770942195 chrY 59373566 372429 0.006272639915210752 0.1793897276389647