BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549112.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,318,885 number of mapped reads = 9,539,972 (84.28%) number of secondary alignments = 0 number of mapped bases = 378,615,022 bp number of sequenced bases = 378,579,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 427,004 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9656 >>>>>>> ACTG content number of A's = 114,685,456 bp (30.29%) number of C's = 73,772,585 bp (19.49%) number of T's = 115,663,351 bp (30.55%) number of G's = 74,456,197 bp (19.67%) number of N's = 1,542 bp (0%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,142,385 number of insertions = 9,722 mapped reads with insertion percentage = 0.1% number of deletions = 28,804 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.1223X std coverageData = 1.0175X There is a 9.45% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 29468608 0.11822882479398115 1.5759458945748555 chr2 243199373 33307137 0.13695404140700643 0.7193968236807654 chr3 198022430 27226204 0.13749050549475633 0.4583796960944046 chr4 191154276 27763776 0.1452427671563047 0.48606718328902654 chr5 180915260 25536941 0.14115415692407596 0.47217342595839107 chr6 171115067 23350078 0.13645834004786966 0.5341728035150987 chr7 159138663 21319746 0.1339696186840529 1.1404644989046404 chr8 146364022 20769676 0.1419042447467042 3.1173265185129813 chr9 141213431 15942580 0.11289705155595292 0.6788527054960904 chr10 135534747 17446505 0.12872348520339216 0.6575465018437162 chr11 135006516 17439672 0.12917652063549287 0.6706120768540111 chr12 133851895 17380343 0.12984756771654224 0.4700645504986721 chr13 115169878 13548898 0.11764272251812231 0.4183026796002635 chr14 107349540 12100454 0.11272012902896464 0.5478138620012337 chr15 102531392 10566108 0.10305241930198314 0.3921799402939799 chr16 90354753 9263434 0.10252292981200446 0.4728481907870927 chr17 81195210 7929977 0.09766557657773162 0.43747971766276333 chr18 78077248 10988230 0.14073536505794876 1.474736978044142 chr19 59128983 5133116 0.08681218143055158 1.249937705693826 chr20 63025520 7108779 0.11279207216378381 0.44372190234849357 chr21 48129895 5113542 0.10624461158703961 0.48077498222204723 chr22 51304566 3129892 0.061006110060457384 0.32558992042527196 chrMT 16571 93015 5.613119304809607 6.621618143271709 chrX 155270560 13667308 0.08802253305455973 0.4732509403965182 chrY 59373566 3021003 0.050881279389551906 0.3811234349007231