BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013354.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 = 3,196,747 number of mapped reads = 2,792,826 (87.36%) number of supplementary alignments = 20,375 (0.64%) number of secondary alignments = 0 number of mapped bases = 181,734,049 bp number of sequenced bases = 181,665,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,613 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5733 >>>>>>> ACTG content number of A's = 50,657,209 bp (27.88%) number of C's = 35,466,376 bp (19.52%) number of T's = 54,171,916 bp (29.82%) number of G's = 41,328,499 bp (22.75%) number of N's = 41,375 bp (0.02%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,404,932 number of insertions = 13,599 mapped reads with insertion percentage = 0.48% number of deletions = 38,963 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.4285X There is a 5.06% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 13465284 0.05402307101975084 0.5646811218183376 chr2 243199373 18409104 0.0756955240998915 0.5732550071140083 chr3 198022430 11334892 0.05724044493343507 0.26711952729489963 chr4 191154276 11062726 0.0578732855549619 0.28817578309307673 chr5 180915260 9709163 0.05366691013240121 0.27175273209495465 chr6 171115067 9578643 0.05597778832649494 0.3203546451215554 chr7 159138663 10948955 0.06880135093255119 0.8046676263477424 chr8 146364022 9764502 0.06671381304348141 0.41755774723500766 chr9 141213431 6644304 0.04705150177960055 0.36763495535853735 chr10 135534747 8582498 0.06332323031524897 0.41107784572673517 chr11 135006516 7725570 0.057223682448038285 0.34850937423479295 chr12 133851895 9041120 0.06754570041761455 0.29726401329774826 chr13 115169878 4394878 0.03815996054107134 0.22951926146030285 chr14 107349540 6119639 0.057006662534371366 0.29401068237948774 chr15 102531392 5228020 0.0509894569655311 0.2684366546035612 chr16 90354753 6097808 0.06748740710961824 0.3350254998510207 chr17 81195210 4969819 0.06120827817305972 0.30298995262642703 chr18 78077248 4282177 0.05484538850549651 0.6326338919580111 chr19 59128983 4033741 0.06821935361208563 0.4919430541746632 chr20 63025520 4358483 0.06915425687880083 0.3032913705949072 chr21 48129895 3000764 0.06234719606182394 0.3078357515025995 chr22 51304566 1975047 0.038496515105497627 0.2181092791317871 chrMT 16571 586285 35.38018224609257 28.482159323473237 chrX 155270560 9982565 0.06429142137440606 0.30844055679725313 chrY 59373566 438062 0.00737806450769691 0.15505388445121168