BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230369.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 = 2,387,083 number of mapped reads = 1,782,801 (74.69%) number of supplementary alignments = 16,022 (0.67%) number of secondary alignments = 0 number of mapped bases = 111,115,091 bp number of sequenced bases = 111,056,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,774 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1172 >>>>>>> ACTG content number of A's = 30,020,506 bp (27.03%) number of C's = 19,930,339 bp (17.95%) number of T's = 35,709,891 bp (32.15%) number of G's = 25,346,968 bp (22.82%) number of N's = 48,759 bp (0.04%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,121,316 number of insertions = 8,924 mapped reads with insertion percentage = 0.5% number of deletions = 36,789 mapped reads with deletion percentage = 2.04% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3417X There is a 2.31% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 7476129 0.029994424768153335 0.45613963425390863 chr2 243199373 10364674 0.04261801283509065 0.4208003968773691 chr3 198022430 7719545 0.038983184884661806 0.28695369146081867 chr4 191154276 6179979 0.032329797320359184 0.2702168564670006 chr5 180915260 6206507 0.03430615526849421 0.2690652070626157 chr6 171115067 6956467 0.040653737405835805 0.3201435805788637 chr7 159138663 6514123 0.04093362905782361 0.47845328370706164 chr8 146364022 5340218 0.03648586535835972 0.3662459533461591 chr9 141213431 5041571 0.035701781086248094 0.3353946513871142 chr10 135534747 6814743 0.05028041259412245 0.35121528818453635 chr11 135006516 5139797 0.03807073282299945 0.3501849753121152 chr12 133851895 4198708 0.03136831196898632 0.26404883159651393 chr13 115169878 3421811 0.02971098918764158 0.256578986640806 chr14 107349540 4001349 0.03727402092267931 0.3010962297922418 chr15 102531392 3373941 0.032906419528567404 0.2991078126354747 chr16 90354753 3261723 0.036099074942963987 0.2851972483117891 chr17 81195210 3152450 0.03882556618795616 0.2981169790078536 chr18 78077248 2570795 0.03292630139832797 0.4595603066710494 chr19 59128983 1633904 0.02763287844812078 0.33558724648988614 chr20 63025520 2077648 0.03296518616585789 0.2674316660353132 chr21 48129895 1483154 0.03081565002375343 0.2606237917564784 chr22 51304566 1050121 0.0204683731268675 0.2010720438952166 chrMT 16571 17938 1.0824935127632611 1.4970126202476772 chrX 155270560 6846571 0.04409445679850707 0.3234875517286009 chrY 59373566 271225 0.004568110327077205 0.10483208534984208