BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,399,781 number of mapped reads = 2,826,077 (83.13%) number of supplementary alignments = 31,985 (0.94%) number of secondary alignments = 0 number of mapped bases = 188,169,998 bp number of sequenced bases = 188,094,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,837 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5199 >>>>>>> ACTG content number of A's = 54,845,942 bp (29.16%) number of C's = 34,226,106 bp (18.2%) number of T's = 58,572,337 bp (31.14%) number of G's = 40,431,551 bp (21.5%) number of N's = 18,119 bp (0.01%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,754,628 number of insertions = 15,841 mapped reads with insertion percentage = 0.56% number of deletions = 44,169 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.4965X There is a 5.2% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 19105356 0.07665118715993088 0.9124531243613301 chr2 243199373 19363553 0.07962007780340782 0.6656760596060914 chr3 198022430 15632307 0.07894210266988441 0.3169866256826257 chr4 191154276 13862738 0.07252120271690914 0.3066111159236394 chr5 180915260 9123848 0.050431610909991785 0.2533861163437549 chr6 171115067 13866821 0.08103798948341585 0.4729565172796244 chr7 159138663 10506910 0.06602361614663056 0.6333039539699499 chr8 146364022 15041107 0.10276505656560872 0.6346270958945458 chr9 141213431 4013273 0.028419910001336913 0.42624191515416354 chr10 135534747 5009088 0.03695796178377785 0.35689375882389407 chr11 135006516 6548896 0.048507999421302 0.3828576369191261 chr12 133851895 6120061 0.045722632466279244 0.24746025794676524 chr13 115169878 3102527 0.02693870180187219 0.18152144495358727 chr14 107349540 2885338 0.026877972648974555 0.2451312297108124 chr15 102531392 3857417 0.03762181440002297 0.2197741010236644 chr16 90354753 7367954 0.08154473069059245 0.3693567135299449 chr17 81195210 3361321 0.04139802089310441 0.2772548459974605 chr18 78077248 7306198 0.09357653077116652 0.9923009551940664 chr19 59128983 3092675 0.05230387608729885 0.6248973055062524 chr20 63025520 4061609 0.06444387924129781 0.3093949954640017 chr21 48129895 3776874 0.07847251692529145 0.3288790792623113 chr22 51304566 2722314 0.05306182689470563 0.25843821989520144 chrMT 16571 44008 2.655723854927283 2.358776870923043 chrX 155270560 8078764 0.05203023676864436 0.3186690886864206 chrY 59373566 319041 0.005373451882610521 0.10287612114062213