BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081170.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 = 2,432,317 number of mapped reads = 2,132,840 (87.69%) number of supplementary alignments = 20,714 (0.85%) number of secondary alignments = 0 number of mapped bases = 141,839,366 bp number of sequenced bases = 141,789,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,726 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6205 >>>>>>> ACTG content number of A's = 39,521,516 bp (27.87%) number of C's = 26,248,259 bp (18.51%) number of T's = 44,673,631 bp (31.51%) number of G's = 31,304,496 bp (22.08%) number of N's = 41,812 bp (0.03%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,180,932 number of insertions = 10,767 mapped reads with insertion percentage = 0.5% number of deletions = 30,896 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.3572X There is a 3.92% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% 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% 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 10904124 0.04374763022155118 0.5990138931364178 chr2 243199373 11923381 0.04902718643110975 0.43810710192993674 chr3 198022430 9581143 0.04838413002001844 0.24752438567232177 chr4 191154276 10019969 0.05241823102089539 0.2655526332250418 chr5 180915260 8981101 0.04964258404736007 0.25293098519809665 chr6 171115067 9610921 0.05616642162785116 0.3530791572614795 chr7 159138663 7429536 0.04668592697677748 0.4272670580422452 chr8 146364022 7918113 0.05409876615716395 0.4826757804021025 chr9 141213431 5927159 0.04197305424864296 0.32680274352825334 chr10 135534747 7504392 0.05536876827607905 0.3343783402260819 chr11 135006516 5978025 0.044279529441378966 0.30483657656487867 chr12 133851895 6451629 0.04819975839714485 0.252766385795472 chr13 115169878 4248497 0.0368889598024928 0.2169903293928197 chr14 107349540 4539259 0.042284848169819825 0.2487167268064432 chr15 102531392 3331453 0.03249202936794226 0.20959213105613766 chr16 90354753 3528364 0.03905012058413795 0.24323036856085886 chr17 81195210 3382330 0.04165676768370942 0.30421245793789825 chr18 78077248 2865952 0.03670662162682783 0.5419247124489908 chr19 59128983 2522127 0.04265466564848579 0.4281333344688361 chr20 63025520 2658652 0.042183737635167466 0.23957308650540998 chr21 48129895 1881149 0.03908483490354592 0.23628862397235476 chr22 51304566 1503759 0.02931043213580639 0.19090716074714248 chrMT 16571 41669 2.514573652766882 2.2949424337355553 chrX 155270560 8780890 0.0565521886441319 0.2943766773115554 chrY 59373566 325772 0.005486818831127643 0.10935262303178393