BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013283.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 = 2,782,969 number of mapped reads = 2,466,104 (88.61%) number of supplementary alignments = 16,639 (0.6%) number of secondary alignments = 0 number of mapped bases = 157,639,971 bp number of sequenced bases = 157,562,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,723 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5859 >>>>>>> ACTG content number of A's = 42,230,250 bp (26.8%) number of C's = 29,917,072 bp (18.99%) number of T's = 48,073,077 bp (30.51%) number of G's = 37,324,815 bp (23.69%) number of N's = 17,146 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,264,783 number of insertions = 11,006 mapped reads with insertion percentage = 0.44% number of deletions = 44,860 mapped reads with deletion percentage = 1.8% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.447X There is a 4.32% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11846870 0.04752995179097267 0.7596424545656653 chr2 243199373 18534830 0.07621249089322282 0.6520463218678134 chr3 198022430 8944930 0.04517129700913174 0.24149095395542627 chr4 191154276 8111355 0.04243355246732749 0.24403661327238071 chr5 180915260 8098104 0.044761862542717516 0.24544714608262266 chr6 171115067 7194388 0.04204415266365761 0.31614953718378713 chr7 159138663 8840692 0.05555338868217084 0.7356097848137604 chr8 146364022 8899512 0.06080395904944454 0.4325607156773363 chr9 141213431 4811126 0.03406988957020667 0.3860566905596037 chr10 135534747 8108577 0.059826555030939775 0.4496277441161587 chr11 135006516 7169752 0.0531067107901666 0.38343398092660574 chr12 133851895 8536916 0.0637788206136342 0.2955534720454448 chr13 115169878 4520167 0.0392478231156935 0.22293530210783052 chr14 107349540 5512043 0.051346684857708755 0.2763976988766014 chr15 102531392 3731271 0.0363914985178393 0.2306700164870543 chr16 90354753 5508141 0.0609612756066081 0.30812895267899304 chr17 81195210 5124028 0.06310751582513303 0.3657344718212112 chr18 78077248 3749165 0.048018662235636174 0.681334664050887 chr19 59128983 3308310 0.05595073400805828 0.6095380924590199 chr20 63025520 4152319 0.06588313749731854 0.2994020123247255 chr21 48129895 3007010 0.06247696987496025 0.30057913981736445 chr22 51304566 1716561 0.033458250090255125 0.20751065906499594 chrMT 16571 62736 3.785891014422787 2.8565969794002948 chrX 155270560 7810253 0.05030092633143076 0.3209480460915246 chrY 59373566 340915 0.005741864990895107 0.10976242982265513