BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708543.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 21,888,688 number of mapped reads = 21,117,546 (96.48%) number of supplementary alignments = 497 (0%) number of secondary alignments = 0 number of mapped bases = 1,053,124,991 bp number of sequenced bases = 1,053,036,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,234 duplication rate = 0.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3899 >>>>>>> ACTG content number of A's = 324,037,757 bp (30.77%) number of C's = 200,652,462 bp (19.05%) number of T's = 324,232,822 bp (30.79%) number of G's = 203,690,242 bp (19.34%) number of N's = 423,205 bp (0.04%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,686,899 number of insertions = 55,826 mapped reads with insertion percentage = 0.26% number of deletions = 53,330 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.3402X std coverageData = 0.6446X There is a 26.44% of reference with a coverageData >= 1X There is a 6.06% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.04% 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 82970984 0.3328817543848767 0.6539804940492461 chr2 243199373 95542498 0.39285667895204646 0.6788436824300174 chr3 198022430 81405254 0.41109107690477287 0.6908164513124971 chr4 191154276 87367519 0.45705239154576904 0.7272648955888936 chr5 180915260 74271792 0.41053359456797617 0.6905802047296252 chr6 171115067 70697423 0.4131572060805142 0.6958703503647105 chr7 159138663 59844007 0.376049451917288 0.6735099863633066 chr8 146364022 59643804 0.4075031772493926 0.6910967375758882 chr9 141213431 43910407 0.3109506417983712 0.6221216522631937 chr10 135534747 46007661 0.33945288583450856 0.6321099218958235 chr11 135006516 47869153 0.35456920464490765 0.6585647673117045 chr12 133851895 49013939 0.3661803891532503 0.667604676705605 chr13 115169878 44006058 0.3820969403128134 0.6843343009432602 chr14 107349540 34482199 0.3212142222500441 0.6367376671256187 chr15 102531392 27959608 0.27269314748013956 0.5850407446271003 chr16 90354753 19657058 0.21755422207838918 0.5175841839173326 chr17 81195210 16514280 0.2033898305084746 0.5008601320087357 chr18 78077248 31461099 0.4029483595528367 0.6885714224735126 chr19 59128983 7381361 0.12483490541347549 0.38300106757585467 chr20 63025520 16187943 0.2568474325955581 0.561759374650267 chr21 48129895 13852181 0.28780825306184443 0.6213339948016053 chr22 51304566 5546397 0.10810727840481099 0.3646011047700602 chrMT 16571 3849 0.2322732484460805 0.48169562180021436 chrX 155270560 32724855 0.2107602046389219 0.4817540146252662 chrY 59373566 4803662 0.08090573505387903 0.3172774302747572