BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063556.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 = 2,931,451 number of mapped reads = 2,619,918 (89.37%) number of supplementary alignments = 24,895 (0.85%) number of secondary alignments = 0 number of mapped bases = 170,616,441 bp number of sequenced bases = 170,544,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,744 duplication rate = 5.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1576 >>>>>>> ACTG content number of A's = 47,271,233 bp (27.72%) number of C's = 30,806,671 bp (18.06%) number of T's = 54,598,724 bp (32.01%) number of G's = 37,863,007 bp (22.2%) number of N's = 4,534 bp (0%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,368,042 number of insertions = 12,232 mapped reads with insertion percentage = 0.46% number of deletions = 45,050 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 0.5789X There is a 4.28% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15860551 0.06363294477007542 1.0798590288026306 chr2 243199373 8111677 0.03335402102373019 0.5747909605893115 chr3 198022430 19872090 0.1003527226688411 0.39042941757175226 chr4 191154276 19853281 0.10385998898606903 0.4069607320717546 chr5 180915260 8430888 0.046601309364395244 0.2703706353144802 chr6 171115067 10403296 0.06079707755951146 0.37001540325409604 chr7 159138663 12668881 0.07960907023581064 0.9408479641458237 chr8 146364022 8586690 0.05866667151303071 1.1886081341334591 chr9 141213431 1462634 0.01035761251350093 0.3695818487815138 chr10 135534747 11670399 0.08610632519201884 0.47445831009933925 chr11 135006516 5695148 0.042184245388570726 0.36242922005284917 chr12 133851895 6411493 0.04789990459231078 0.31005098416056986 chr13 115169878 2501016 0.02171588650983897 0.19031697298038006 chr14 107349540 4663966 0.04344653922131385 0.31691111576071673 chr15 102531392 624532 0.006091129631791208 0.13422059339073295 chr16 90354753 2525077 0.027946255356372896 0.23620671578097802 chr17 81195210 3185422 0.03923164925615686 0.25136892150831663 chr18 78077248 2459081 0.031495487648335145 0.6877408608516954 chr19 59128983 5058309 0.08554703198598901 0.7159813452135326 chr20 63025520 1418042 0.02249948909584562 0.23560448301045034 chr21 48129895 2282599 0.047425804689580145 0.26990544853778686 chr22 51304566 2064387 0.04023788058162309 0.24524415183833764 chrMT 16571 53369 3.220626395510229 3.1103080917072052 chrX 155270560 14494585 0.09335050379157517 0.4562243719969228 chrY 59373566 259028 0.0043626822077690265 0.08351329686718952