BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124939.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,284,810 number of mapped reads = 6,198,769 (98.63%) number of supplementary alignments = 30,979 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,104,274 number of mapped paired reads (second in pair) = 3,094,495 number of mapped paired reads (both in pair) = 6,173,524 number of mapped paired reads (singletons) = 25,245 number of mapped bases = 546,340,544 bp number of sequenced bases = 546,059,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 559,574 duplication rate = 6.06% >>>>>>> Insert size mean insert size = 48,516.3736 std insert size = 2,086,885.8131 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6993 >>>>>>> ACTG content number of A's = 155,743,428 bp (28.52%) number of C's = 100,987,836 bp (18.49%) number of T's = 164,533,179 bp (30.13%) number of G's = 124,786,723 bp (22.85%) number of N's = 7,882 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 3,995,090 number of insertions = 70,301 mapped reads with insertion percentage = 1.11% number of deletions = 170,071 mapped reads with deletion percentage = 2.69% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.1765X std coverageData = 1.7426X There is a 11.35% of reference with a coverageData >= 1X There is a 3.48% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 49203758 0.19740676192738552 1.9452827445342458 chr2 243199373 36728229 0.1510210678051378 2.0338136162169502 chr3 198022430 48821226 0.24654391929237512 0.7676842503098716 chr4 191154276 35349809 0.18492816242311 0.9592352524241086 chr5 180915260 34074174 0.18834328292704552 0.5942097098875901 chr6 171115067 32691651 0.19105068637819017 2.256240527214679 chr7 159138663 31174625 0.1958959841204648 2.3095283580922517 chr8 146364022 38561331 0.26346181577327793 0.9448538770059169 chr9 141213431 24075787 0.1704921892309238 2.6598681653137555 chr10 135534747 25688312 0.18953303539202387 3.6623113468446147 chr11 135006516 26807341 0.19856331230708893 1.5184243122755847 chr12 133851895 21893074 0.16356192790546598 0.5472526537855541 chr13 115169878 9370995 0.08136671812746038 0.36508141137500755 chr14 107349540 21575288 0.20098165301872742 0.7678985021619211 chr15 102531392 10130763 0.09880645139393017 0.417182301340751 chr16 90354753 15167013 0.16786071010564324 2.8157520482150264 chr17 81195210 8623228 0.10620365413181393 1.223823303944759 chr18 78077248 18257664 0.23384102882314706 2.769329322847968 chr19 59128983 10907801 0.18447469323123653 1.3030829148920526 chr20 63025520 12475144 0.19793797813964883 0.6440836434813595 chr21 48129895 6585303 0.13682354802560862 0.6490731675813967 chr22 51304566 4715823 0.09191819301229447 0.42428597194279605 chrMT 16571 257507 15.539617403898376 9.85948521333252 chrX 155270560 16512636 0.10634750077542066 0.7650914161159724 chrY 59373566 6692062 0.11271113478344892 2.1845186628451194