BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238545.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 = 4,673,576 number of mapped reads = 4,236,089 (90.64%) number of supplementary alignments = 37,609 (0.8%) number of secondary alignments = 0 number of mapped bases = 263,405,171 bp number of sequenced bases = 263,249,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 950,997 duplication rate = 16.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8122 >>>>>>> ACTG content number of A's = 66,261,422 bp (25.17%) number of C's = 46,786,741 bp (17.77%) number of T's = 87,380,651 bp (33.19%) number of G's = 62,802,052 bp (23.86%) number of N's = 18,173 bp (0.01%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,600,599 number of insertions = 16,649 mapped reads with insertion percentage = 0.39% number of deletions = 90,071 mapped reads with deletion percentage = 2.1% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0851X std coverageData = 0.984X There is a 4.64% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 25503914 0.1023223689380497 0.7028579939941602 chr2 243199373 28828602 0.1185389651477432 2.137621500846954 chr3 198022430 12178617 0.06150119963682902 0.422658888683804 chr4 191154276 13154957 0.06881853377949024 0.46125847281038956 chr5 180915260 11952478 0.06606672096096261 0.4434857628795072 chr6 171115067 29896953 0.17471841331190316 1.4273878120804226 chr7 159138663 15862136 0.09967493568800437 1.7785975199047528 chr8 146364022 18696484 0.12773961622891178 0.9243642311152094 chr9 141213431 13892200 0.0983773278619652 0.7668007889689996 chr10 135534747 17504299 0.12914989984081351 0.9270420529949909 chr11 135006516 6911686 0.051195203052273416 0.4364390931834935 chr12 133851895 10287289 0.07685575912092989 0.49389565242504324 chr13 115169878 6196205 0.053800569277324406 0.5108534313384837 chr14 107349540 5800008 0.05402918354377671 0.4903990534774243 chr15 102531392 5048131 0.04923497966359415 0.5178956370594485 chr16 90354753 10427216 0.11540307126953243 0.659773576962514 chr17 81195210 1641457 0.020216180240189046 0.24512235998348292 chr18 78077248 8942774 0.11453751546161053 1.6051689054501022 chr19 59128983 2097660 0.03547600336707973 0.5350887062581952 chr20 63025520 7578747 0.12024886109626703 0.5939166068953246 chr21 48129895 1879969 0.03906031791675423 0.3905121514683381 chr22 51304566 942857 0.01837764303473496 0.21616967619258834 chrMT 16571 175246 10.575463158529962 6.918874533771948 chrX 155270560 7490343 0.04824058726908694 0.40451851035847664 chrY 59373566 514943 0.008672933675568687 0.32406395336301524