BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549039.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,939,751 number of mapped reads = 7,642,483 (85.49%) number of secondary alignments = 0 number of mapped bases = 302,747,066 bp number of sequenced bases = 302,718,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,886 duplication rate = 4.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8077 >>>>>>> ACTG content number of A's = 85,647,177 bp (28.29%) number of C's = 64,133,577 bp (21.19%) number of T's = 87,587,477 bp (28.93%) number of G's = 65,350,468 bp (21.59%) number of N's = 250 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 770,684 number of insertions = 8,366 mapped reads with insertion percentage = 0.11% number of deletions = 21,378 mapped reads with deletion percentage = 0.28% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.0978X std coverageData = 0.6186X There is a 6.61% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 25641425 0.10287406666080082 0.7532114084543282 chr2 243199373 24247582 0.09970248566389191 0.6329947488655312 chr3 198022430 19998917 0.10099319051887203 0.44811023573782194 chr4 191154276 21943225 0.11479327305239041 0.5212499518907845 chr5 180915260 17692450 0.09779412748266786 0.44152336767298234 chr6 171115067 16953131 0.09907444912492715 0.4607371665785006 chr7 159138663 16203442 0.1018196439164504 0.7330067447209401 chr8 146364022 14872268 0.10161150121988312 1.228242590898127 chr9 141213431 13235519 0.09372705490032318 0.6052641043361394 chr10 135534747 15464243 0.11409799584456376 0.6153619694458122 chr11 135006516 12849514 0.09517699130907134 0.5017480324324071 chr12 133851895 14621221 0.10923432200941197 0.47892535692163973 chr13 115169878 10612513 0.0921466027775075 0.43441195833610247 chr14 107349540 9619606 0.08961012781237815 0.49700378060655515 chr15 102531392 9518444 0.09283443650116445 0.43481180167648714 chr16 90354753 8791248 0.09729701767874901 0.49427537478258465 chr17 81195210 8401173 0.10346882531617321 0.47884790033084984 chr18 78077248 7422440 0.09506533836848348 1.0347103229450896 chr19 59128983 5814214 0.09833103336142278 0.7313722745223181 chr20 63025520 6866386 0.10894612214226872 0.4898657757980662 chr21 48129895 4232624 0.08794168364589201 0.5291121432546212 chr22 51304566 3738224 0.07286337828098965 0.5511724860838416 chrMT 16571 26083 1.5740148452115141 2.4457911441787292 chrX 155270560 11237009 0.07237050603797655 0.42787868851725225 chrY 59373566 2744165 0.0462186320424143 0.44216085259417354