BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238529.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 = 1,812,102 number of mapped reads = 1,562,371 (86.22%) number of supplementary alignments = 13,833 (0.76%) number of secondary alignments = 0 number of mapped bases = 95,176,497 bp number of sequenced bases = 95,122,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,379 duplication rate = 18.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8923 >>>>>>> ACTG content number of A's = 23,419,707 bp (24.62%) number of C's = 16,846,569 bp (17.71%) number of T's = 31,960,362 bp (33.6%) number of G's = 22,889,178 bp (24.06%) number of N's = 6,335 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 643,394 number of insertions = 5,769 mapped reads with insertion percentage = 0.37% number of deletions = 32,609 mapped reads with deletion percentage = 2.06% homopolymer indels = 39.14% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.5763X There is a 1.43% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% 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% 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 12576995 0.050459232356335836 0.5656465676939987 chr2 243199373 3750155 0.01542008498516976 1.4244129321056913 chr3 198022430 3113421 0.01572256738794691 0.24186591148147887 chr4 191154276 7387989 0.038649352526123976 0.3772647906560677 chr5 180915260 5565168 0.03076118620397196 0.3550216605101549 chr6 171115067 4724197 0.027608305234745927 0.5500000394659248 chr7 159138663 2754559 0.01730917520653042 0.29583729453312885 chr8 146364022 8444532 0.05769540823358899 0.5198403759893263 chr9 141213431 6685849 0.04734570184049986 0.4869781013581334 chr10 135534747 10467145 0.07722849846025094 0.5820662553870376 chr11 135006516 916289 0.006786998340139375 0.15627097212213345 chr12 133851895 4186401 0.031276367062266844 0.3521279479071929 chr13 115169878 3892954 0.03380184183228882 0.45800948897104654 chr14 107349540 1509780 0.01406414969267684 0.26403592004185156 chr15 102531392 707477 0.006900101385534685 0.3393135388766804 chr16 90354753 2476678 0.027410600082100826 0.36064439028266854 chr17 81195210 1238071 0.015248079289406358 0.23457418387065504 chr18 78077248 6872238 0.08801844552717841 1.0869212142133773 chr19 59128983 1351019 0.022848676426584235 0.3801741411983408 chr20 63025520 2932899 0.04653510197139191 0.4294541802019686 chr21 48129895 1558447 0.03238002077502974 0.35542187688851107 chr22 51304566 590105 0.01150199769743691 0.19825536439347138 chrMT 16571 101550 6.128175728682638 5.227440937419485 chrX 155270560 1198853 0.007721058003526232 0.16839921843572245 chrY 59373566 173726 0.002925982246038582 0.1787747407153121