BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053672.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,264,175 number of mapped reads = 5,674,824 (78.12%) number of supplementary alignments = 167 (0%) number of secondary alignments = 0 number of mapped bases = 265,088,589 bp number of sequenced bases = 265,036,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,093,412 duplication rate = 13.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.405 >>>>>>> ACTG content number of A's = 79,246,905 bp (29.9%) number of C's = 54,160,711 bp (20.44%) number of T's = 75,562,488 bp (28.51%) number of G's = 55,903,215 bp (21.09%) number of N's = 163,613 bp (0.06%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,872,830 number of insertions = 12,544 mapped reads with insertion percentage = 0.22% number of deletions = 36,433 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0856X std coverageData = 0.6753X There is a 4.3% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 21520189 0.08633956021317195 0.7117966823630816 chr2 243199373 22420553 0.09219001152605767 0.7351107016105695 chr3 198022430 18951068 0.09570162329590642 0.6953453872057825 chr4 191154276 18155337 0.09497740453370764 0.7132330996745596 chr5 180915260 16470882 0.09104197180492127 0.6718449652207995 chr6 171115067 15074989 0.08809854832947002 0.6738938806782906 chr7 159138663 12937481 0.08129690645949439 0.6710810272997908 chr8 146364022 11487142 0.07848337209536371 0.6429456134661418 chr9 141213431 10700747 0.07577711924583151 0.6247981503690573 chr10 135534747 12953123 0.09557049602933188 0.6995264207139216 chr11 135006516 11714624 0.08677080445509756 0.6901040540236898 chr12 133851895 13164675 0.09835254853881598 0.709877910072764 chr13 115169878 9726298 0.08445175221944752 0.6503577229896206 chr14 107349540 8535909 0.07951509619882861 0.6810844482387789 chr15 102531392 8312087 0.08106870332941545 0.6237570649673702 chr16 90354753 7438404 0.08232443510747021 0.6599428691039242 chr17 81195210 6378692 0.0785599544603678 0.5966247271430878 chr18 78077248 7977966 0.10218042008857689 0.7648502781854132 chr19 59128983 5289928 0.08946421419086474 0.703536016320584 chr20 63025520 5552393 0.08809753572838432 0.6678376832051753 chr21 48129895 3018776 0.06272143332122375 0.5962780109955874 chr22 51304566 2691467 0.052460574366811716 0.5001450359480403 chrMT 16571 10575 0.6381630559411019 1.8830450792127 chrX 155270560 13968441 0.08996194127206085 0.6860245588048434 chrY 59373566 636843 0.010726035892807921 0.22298789255710216