BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004122.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 = 4,118,739 number of mapped reads = 3,436,590 (83.44%) number of supplementary alignments = 22,146 (0.54%) number of secondary alignments = 0 number of mapped bases = 227,058,011 bp number of sequenced bases = 226,948,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 259,784 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6226 >>>>>>> ACTG content number of A's = 63,006,896 bp (27.76%) number of C's = 39,712,215 bp (17.5%) number of T's = 75,404,314 bp (33.23%) number of G's = 48,801,820 bp (21.5%) number of N's = 23,030 bp (0.01%) GC percentage = 39% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 2,195,249 number of insertions = 19,467 mapped reads with insertion percentage = 0.56% number of deletions = 66,449 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0733X std coverageData = 0.6722X There is a 5.28% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 21601845 0.08666716621741136 1.4024928508740677 chr2 243199373 19167570 0.07881422457450168 0.705961500780605 chr3 198022430 18664992 0.09425695866877302 0.40522839711894565 chr4 191154276 18630613 0.09746375226259653 0.41973284019397245 chr5 180915260 7646045 0.042263129157816756 0.2764831559095899 chr6 171115067 12199283 0.07129286283130169 0.40155022284211855 chr7 159138663 10747235 0.06753377713120538 0.5237995737422985 chr8 146364022 13802387 0.094301774516691 1.1972308516988772 chr9 141213431 4115658 0.029144947267799193 0.4776635009722873 chr10 135534747 20130108 0.14852359594547368 0.7359922977581937 chr11 135006516 6164385 0.04565990725958738 0.379801463887297 chr12 133851895 12659319 0.0945770622074495 0.40421742003662403 chr13 115169878 13273763 0.11525377321316603 0.44297323578279857 chr14 107349540 2603794 0.024255287912738146 0.2800378011429399 chr15 102531392 3703191 0.03611763117387502 0.25134162232086427 chr16 90354753 5634364 0.06235824694247131 0.3950779443145301 chr17 81195210 2842184 0.03500433092050627 0.27875383616002813 chr18 78077248 4891723 0.0626523491196821 1.2503463472525187 chr19 59128983 3210192 0.0542913447369795 0.8330068860526944 chr20 63025520 2408361 0.03821247329653131 0.3164999742923509 chr21 48129895 4682211 0.09728280105327468 0.427924116252193 chr22 51304566 3186423 0.0621079807984342 0.3202373324659971 chrMT 16571 139129 8.395932653430693 6.403708559032851 chrX 155270560 14433073 0.09295434369528904 0.4522816062183159 chrY 59373566 520163 0.008760851588398783 0.16170010944776736