BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472826.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,792,904 number of mapped reads = 1,936,085 (69.32%) number of supplementary alignments = 13,138 (0.47%) number of secondary alignments = 0 number of mapped bases = 124,496,620 bp number of sequenced bases = 124,444,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,036 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3063 >>>>>>> ACTG content number of A's = 33,988,731 bp (27.31%) number of C's = 24,032,557 bp (19.31%) number of T's = 37,660,785 bp (30.26%) number of G's = 28,759,788 bp (23.11%) number of N's = 2,950 bp (0%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,072,766 number of insertions = 10,027 mapped reads with insertion percentage = 0.51% number of deletions = 29,172 mapped reads with deletion percentage = 1.49% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3084X There is a 3.55% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9126918 0.03661743334232254 0.3966465768935465 chr2 243199373 12127958 0.049868376922172414 0.4548467730334631 chr3 198022430 9032580 0.04561392363481248 0.23414045976265863 chr4 191154276 6988634 0.03656017613751941 0.22899523091039306 chr5 180915260 6290427 0.034770018847497995 0.20635915623560702 chr6 171115067 7640611 0.044651889129085284 0.25452557026083267 chr7 159138663 7589313 0.0476899381767459 0.3995115514575609 chr8 146364022 7027216 0.048011908281667744 0.34923787753817387 chr9 141213431 7153314 0.05065604559951525 0.36037384734826367 chr10 135534747 5112483 0.037720828888255495 0.2740482099372028 chr11 135006516 4167158 0.030866347221344487 0.2733665967527258 chr12 133851895 5227972 0.03905788558316638 0.22388399000791626 chr13 115169878 5062832 0.04395968883461004 0.2394325090053304 chr14 107349540 2540498 0.023665662656775242 0.19447511222831176 chr15 102531392 2304354 0.022474619285379447 0.1781573236982777 chr16 90354753 3886155 0.043009967610669025 0.24713260820241276 chr17 81195210 2713652 0.03342133113517411 0.21686088230447978 chr18 78077248 2113842 0.027073725754268387 0.543494030195447 chr19 59128983 2835299 0.04795108686378049 0.3383969660798421 chr20 63025520 5504800 0.08734239717498563 0.34132866772814086 chr21 48129895 1834536 0.03811635159395216 0.24339771519115946 chr22 51304566 1413431 0.027549809114455818 0.19037332643274685 chrMT 16571 66292 4.0004827711061495 3.5575988341924525 chrX 155270560 6095699 0.03925856260195107 0.2452835813760024 chrY 59373566 640646 0.010790087966082414 0.15271449257528572