BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230367.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,880,474 number of mapped reads = 2,737,193 (95.03%) number of supplementary alignments = 19,247 (0.67%) number of secondary alignments = 0 number of mapped bases = 197,704,260 bp number of sequenced bases = 197,627,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,012 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1134 >>>>>>> ACTG content number of A's = 59,222,942 bp (29.97%) number of C's = 40,037,288 bp (20.26%) number of T's = 58,173,059 bp (29.44%) number of G's = 40,080,897 bp (20.28%) number of N's = 113,757 bp (0.06%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,694,375 number of insertions = 17,493 mapped reads with insertion percentage = 0.63% number of deletions = 45,303 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.8583X There is a 3.15% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 14877288 0.05968806793865521 1.9828662118822613 chr2 243199373 19748458 0.0812027504692621 0.8551902491347817 chr3 198022430 12015935 0.060679666439806844 0.42594934175693344 chr4 191154276 12314714 0.0644229062393561 0.5136401255024484 chr5 180915260 11333428 0.06264495322285141 0.4402372704479162 chr6 171115067 11265431 0.06583541237780072 0.4997903091944323 chr7 159138663 10245368 0.06438013118157214 0.7583311786820303 chr8 146364022 10486829 0.07164895345660835 1.1540056942833197 chr9 141213431 9222199 0.06530681206945535 0.7689371912376636 chr10 135534747 9412012 0.0694435353909651 0.7354644562667646 chr11 135006516 8841952 0.06549277962257763 0.6271830152587148 chr12 133851895 7916042 0.05914030578349302 0.43951857979493 chr13 115169878 5793397 0.05030305754079205 0.3911955500017981 chr14 107349540 6438081 0.059973065557616737 0.46880513823208914 chr15 102531392 5227245 0.05098189830486257 0.3910273380826907 chr16 90354753 5161014 0.057119452255046284 0.499700874219966 chr17 81195210 5148188 0.06340507032372969 0.5157561888756359 chr18 78077248 5163924 0.06613865283776395 1.5026466094717439 chr19 59128983 4118747 0.06965699037982777 1.084419135737259 chr20 63025520 4365296 0.06926235594724169 0.49145824776895547 chr21 48129895 2752843 0.05719611480556939 0.4905046264465897 chr22 51304566 1999569 0.03897448425935423 0.331558086202148 chrMT 16571 53420 3.2237040613119303 3.3720745625907114 chrX 155270560 13170949 0.08482579698302112 0.5621076630051155 chrY 59373566 631931 0.01064330547368504 0.34348696810815893