BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013331.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 = 1,242,590 number of mapped reads = 838,745 (67.5%) number of supplementary alignments = 5,334 (0.43%) number of secondary alignments = 0 number of mapped bases = 53,233,629 bp number of sequenced bases = 53,208,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,416 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.446 >>>>>>> ACTG content number of A's = 15,928,850 bp (29.94%) number of C's = 9,377,245 bp (17.62%) number of T's = 16,082,496 bp (30.23%) number of G's = 11,819,071 bp (22.21%) number of N's = 432 bp (0%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 505,809 number of insertions = 3,571 mapped reads with insertion percentage = 0.42% number of deletions = 15,213 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.19% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1606X There is a 1.58% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4196313 0.01683571733207437 0.20129372029315967 chr2 243199373 6418527 0.026392037614340395 0.19420200020687087 chr3 198022430 3494426 0.01764661710292112 0.14201929311611267 chr4 191154276 3349675 0.01752341129946787 0.14310105537814669 chr5 180915260 2574654 0.014231270485419528 0.1279589952516334 chr6 171115067 2712259 0.015850497840730764 0.1447780418618209 chr7 159138663 3280939 0.020616856634016086 0.22702317503650074 chr8 146364022 3192204 0.021810031976300843 0.19939080845212506 chr9 141213431 1829583 0.012956154291017829 0.13755095419993382 chr10 135534747 2466973 0.018201775224474356 0.15702327649093914 chr11 135006516 2275846 0.016857304872603333 0.1556279259655221 chr12 133851895 2754833 0.02058120282869361 0.15513147773843325 chr13 115169878 1108757 0.009627144000274099 0.10434852274083872 chr14 107349540 1819591 0.016950151812480985 0.1415541509199921 chr15 102531392 1531149 0.014933465450269124 0.13338149084914763 chr16 90354753 1582253 0.017511563558809132 0.1426638234627537 chr17 81195210 1195981 0.014729698956379324 0.13459049876809984 chr18 78077248 1177222 0.015077657450221606 0.19301619252101646 chr19 59128983 873734 0.014776746625254826 0.16810667546528876 chr20 63025520 1066325 0.016918940137265033 0.13973610213201199 chr21 48129895 976819 0.020295473322765403 0.15508870008670644 chr22 51304566 408699 0.007966133072834102 0.09401724403748399 chrMT 16571 10296 0.6213264136141452 0.9032313102000978 chrX 155270560 2840124 0.018291452030571666 0.14873831761384307 chrY 59373566 96447 0.0016244097583763117 0.04480870901636096