BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013369.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 = 2,187,732 number of mapped reads = 1,977,619 (90.4%) number of supplementary alignments = 11,652 (0.53%) number of secondary alignments = 0 number of mapped bases = 133,916,501 bp number of sequenced bases = 133,860,376 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,415 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.603 >>>>>>> ACTG content number of A's = 38,104,777 bp (28.47%) number of C's = 24,540,725 bp (18.33%) number of T's = 42,566,550 bp (31.8%) number of G's = 28,619,075 bp (21.38%) number of N's = 29,249 bp (0.02%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,056,487 number of insertions = 10,263 mapped reads with insertion percentage = 0.51% number of deletions = 31,847 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.4637X There is a 3.67% of reference with a coverageData >= 1X There is a 0.46% 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 9536287 0.03825983245995604 0.8287567336271902 chr2 243199373 15212752 0.06255259547893653 0.48567862338127543 chr3 198022430 13055963 0.06593173813693731 0.2892649123360607 chr4 191154276 9842938 0.05149211519600012 0.30538201791068054 chr5 180915260 5660570 0.03128851596045574 0.2025444187637841 chr6 171115067 10667064 0.06233854322132837 0.3863533389495625 chr7 159138663 7947677 0.04994183594466921 0.9615836644643526 chr8 146364022 7945077 0.054282991758726064 0.516410906600984 chr9 141213431 7156207 0.05067653231936557 0.40292536085581215 chr10 135534747 5421288 0.03999924831084091 0.5009610608261946 chr11 135006516 3705740 0.02744860107344745 0.2589011223952584 chr12 133851895 7107602 0.0531004958876376 0.2715909586479452 chr13 115169878 5179528 0.04497293988624352 0.23872966440993884 chr14 107349540 4795686 0.044673558917905004 0.26197651671195404 chr15 102531392 3561156 0.03473234811832068 0.2138941051230956 chr16 90354753 1620509 0.01793496131852632 0.2087924523980251 chr17 81195210 4114716 0.05067683179832899 0.289510535488897 chr18 78077248 2208861 0.028290712807910443 0.7415714533439967 chr19 59128983 1622914 0.027447013590610886 0.5506357396230988 chr20 63025520 1603074 0.025435315726074135 0.2007731171342352 chr21 48129895 1279655 0.02658752943466841 0.23814742622127244 chr22 51304566 956933 0.01865200457986527 0.15073104527846923 chrMT 16571 171408 10.343853720354836 5.985421754758924 chrX 155270560 3309248 0.021312784599991138 0.1972384553645862 chrY 59373566 233648 0.003935219252284763 0.18177825515538593