BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083777.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 = 2,088,200 number of mapped reads = 1,178,749 (56.45%) number of supplementary alignments = 6,516 (0.31%) number of secondary alignments = 0 number of mapped bases = 76,230,154 bp number of sequenced bases = 76,202,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,074 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5913 >>>>>>> ACTG content number of A's = 21,595,410 bp (28.34%) number of C's = 14,268,492 bp (18.72%) number of T's = 22,980,087 bp (30.16%) number of G's = 17,357,658 bp (22.78%) number of N's = 901 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 649,184 number of insertions = 5,637 mapped reads with insertion percentage = 0.48% number of deletions = 17,138 mapped reads with deletion percentage = 1.44% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.226X There is a 2.27% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5946833 0.02385884928246578 0.3681905512203651 chr2 243199373 6655414 0.027366082066338223 0.27270753444685164 chr3 198022430 5017574 0.025338412421259553 0.17003294159989676 chr4 191154276 4817351 0.0252013771326779 0.17519798173737566 chr5 180915260 4663031 0.025774669312030395 0.17043766602073615 chr6 171115067 4396574 0.02569366962875338 0.19552672137709123 chr7 159138663 4074138 0.02560118278736576 0.25327797354815274 chr8 146364022 3907938 0.026700127166497244 0.2253250178465953 chr9 141213431 3234834 0.022907410273177203 0.213262213546625 chr10 135534747 3703468 0.0273248600965773 0.24702071377123988 chr11 135006516 3487391 0.025831279136186287 0.19799689686722285 chr12 133851895 3443040 0.025722758725231346 0.1717493759344476 chr13 115169878 2520259 0.0218829701286998 0.1568412338469383 chr14 107349540 2331029 0.021714382753759354 0.1622619408467066 chr15 102531392 2226223 0.021712599005775712 0.15917204693333498 chr16 90354753 2128293 0.02355485383264785 0.17954090678793286 chr17 81195210 1976661 0.02434455185225828 0.18212313142233474 chr18 78077248 1986232 0.02543931876287443 0.3997875379920821 chr19 59128983 1504007 0.025436037010817522 0.2699951940685658 chr20 63025520 1542918 0.024480845219523775 0.1712088814542453 chr21 48129895 1004327 0.02086700999451588 0.15799135849533558 chr22 51304566 836969 0.016313733167531326 0.13533417338003265 chrMT 16571 26124 1.5764890471305293 1.4244201165575978 chrX 155270560 4606103 0.02966501183482561 0.19978068123542642 chrY 59373566 193423 0.0032577292056198883 0.07963336250563331