BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068149.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 = 4,526,916 number of mapped reads = 4,172,897 (92.18%) number of supplementary alignments = 29,494 (0.65%) number of secondary alignments = 0 number of mapped bases = 262,117,172 bp number of sequenced bases = 261,988,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,237,479 duplication rate = 20.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9869 >>>>>>> ACTG content number of A's = 68,294,581 bp (26.07%) number of C's = 45,957,059 bp (17.54%) number of T's = 86,422,447 bp (32.99%) number of G's = 61,285,077 bp (23.39%) number of N's = 29,092 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,645,629 number of insertions = 17,646 mapped reads with insertion percentage = 0.42% number of deletions = 71,559 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.0847X std coverageData = 0.7981X There is a 3.37% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 20822573 0.0835407066046989 1.1808433135325567 chr2 243199373 25018937 0.10287418380803144 1.0782666948761845 chr3 198022430 19222589 0.09707278614851864 0.6469694053485203 chr4 191154276 14763751 0.07723474101097273 0.622841993699706 chr5 180915260 20058348 0.11087150967806696 0.67949496783703 chr6 171115067 15910083 0.09297885498300393 0.7012839986422993 chr7 159138663 14346746 0.09015248544597865 0.8119259193863896 chr8 146364022 13227712 0.09037543393006787 1.1906987780845244 chr9 141213431 12384458 0.08770028397652911 0.7210882423949017 chr10 135534747 9289964 0.06854304306186516 0.6696204487708188 chr11 135006516 12439667 0.09214123413124742 0.7808576035034771 chr12 133851895 11136644 0.08320124268692647 0.5975469492957414 chr13 115169878 8080267 0.07015955161470258 0.5567278253017072 chr14 107349540 8482071 0.07901357565202421 0.6009909649913724 chr15 102531392 7881213 0.07686634157858697 0.6026319173505673 chr16 90354753 6784257 0.07508467208139012 0.5779497002485287 chr17 81195210 6671386 0.08216477302047744 0.6193973720724809 chr18 78077248 7145134 0.09151365068604878 1.1466432570701244 chr19 59128983 5022162 0.08493570741779881 0.8587991525431269 chr20 63025520 5051262 0.08014629629394569 0.6037660018900755 chr21 48129895 3703243 0.07694267772659799 0.6075461618211732 chr22 51304566 2757064 0.05373915452281577 0.48292456492330293 chrMT 16571 373371 22.531591334258646 16.83805961265138 chrX 155270560 9566637 0.06161269077666751 0.5333485561797198 chrY 59373566 1977633 0.033308307606115486 0.409628876459341