BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238075.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 = 2,550,435 number of mapped reads = 2,311,773 (90.64%) number of supplementary alignments = 19,354 (0.76%) number of secondary alignments = 0 number of mapped bases = 155,365,970 bp number of sequenced bases = 155,294,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,436 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6386 >>>>>>> ACTG content number of A's = 42,576,587 bp (27.42%) number of C's = 29,487,547 bp (18.99%) number of T's = 48,450,266 bp (31.2%) number of G's = 34,757,795 bp (22.38%) number of N's = 21,995 bp (0.01%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,145,252 number of insertions = 10,471 mapped reads with insertion percentage = 0.45% number of deletions = 40,534 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.406X There is a 4.14% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% 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 8714580 0.034963122519161144 0.5783967534524991 chr2 243199373 10919232 0.04489827364809859 0.5285673275894421 chr3 198022430 12683227 0.06404944631777319 0.2938692217564962 chr4 191154276 7853360 0.04108388347012441 0.25602982675626534 chr5 180915260 10435147 0.0576797501769613 0.2825002800704867 chr6 171115067 9058523 0.0529381962606484 0.3493096706561913 chr7 159138663 10131540 0.06366485559829041 0.6402225626069051 chr8 146364022 9099732 0.06217191817808888 0.45734301782497233 chr9 141213431 6070234 0.04298623691113347 0.4311083682676201 chr10 135534747 3217219 0.02373722658736361 0.3248068579578299 chr11 135006516 7059747 0.05229189826659922 0.36670586086707774 chr12 133851895 4548855 0.03398424056678465 0.2229215513520979 chr13 115169878 5088989 0.04418680551176758 0.24386849444812994 chr14 107349540 4457043 0.0415189762340854 0.2694934355186998 chr15 102531392 6557089 0.06395201383786929 0.2982388895198865 chr16 90354753 4056447 0.04489467200469244 0.2894106613062412 chr17 81195210 1925937 0.02371983519717481 0.212188982543521 chr18 78077248 5913706 0.07574173208563909 0.7134147003025268 chr19 59128983 2235971 0.03781514388637464 0.4885342174574621 chr20 63025520 4862781 0.07715574579947933 0.3282476125121843 chr21 48129895 2225935 0.04624849067300064 0.28271144651490204 chr22 51304566 2312312 0.045070296472247716 0.24952710094704886 chrMT 16571 28773 1.7363466296542152 1.9567333481066735 chrX 155270560 15432662 0.09939206762698607 0.4171556601739275 chrY 59373566 476929 0.00803268242301633 0.18511596173553466