BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081964.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 = 2,908,995 number of mapped reads = 2,676,741 (92.02%) number of supplementary alignments = 18,567 (0.64%) number of secondary alignments = 0 number of mapped bases = 189,597,189 bp number of sequenced bases = 189,527,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,046 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6727 >>>>>>> ACTG content number of A's = 56,070,181 bp (29.58%) number of C's = 35,421,309 bp (18.69%) number of T's = 59,975,750 bp (31.64%) number of G's = 38,034,276 bp (20.07%) number of N's = 25,530 bp (0.01%) GC percentage = 38.76% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,449,504 number of insertions = 14,184 mapped reads with insertion percentage = 0.52% number of deletions = 39,234 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0612X std coverageData = 0.4969X There is a 5.06% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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 17405423 0.06983101157449072 0.8658960067165623 chr2 243199373 16775572 0.06897868112513596 0.5770264614606148 chr3 198022430 12161402 0.06141426504058151 0.28809192711440373 chr4 191154276 9959671 0.05210278947670519 0.27718754732592976 chr5 180915260 9934989 0.0549151519888372 0.273316436592196 chr6 171115067 16889651 0.09870347068852797 0.49146409599262475 chr7 159138663 12396092 0.07789491105627801 0.6033763888802883 chr8 146364022 10965976 0.0749226199864882 0.8508279542235322 chr9 141213431 9332959 0.06609115672573666 0.523112957381874 chr10 135534747 7478105 0.055174818011797376 0.4812364251416993 chr11 135006516 8474524 0.06277122209419878 0.37227578052887866 chr12 133851895 8210590 0.06134085737075295 0.2969108706869181 chr13 115169878 5280362 0.04584846395339587 0.24572222339431138 chr14 107349540 4777741 0.044506394717667166 0.26753137064174043 chr15 102531392 4270479 0.04165045374591227 0.23526364649480697 chr16 90354753 3841054 0.04251081290654405 0.3000559277362228 chr17 81195210 4662120 0.05741865807108572 0.3140044012496025 chr18 78077248 5355860 0.06859693620348914 0.8471192864976792 chr19 59128983 3488621 0.05900018608471585 0.5879908899602913 chr20 63025520 4506789 0.07150736717443981 0.31407875106943883 chr21 48129895 2054276 0.042681913185142 0.2694432476079771 chr22 51304566 1364523 0.026596521642927456 0.18382873436021446 chrMT 16571 188312 11.363949067648301 7.571174993826883 chrX 155270560 9434340 0.06076064902451566 0.3263263117444112 chrY 59373566 387758 0.006530818782216989 0.14531611558691407