BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054634.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 = 13,243,310 number of mapped reads = 10,738,044 (81.08%) number of supplementary alignments = 291 (0%) number of secondary alignments = 0 number of mapped bases = 507,907,489 bp number of sequenced bases = 507,797,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,443,015 duplication rate = 16.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0598 >>>>>>> ACTG content number of A's = 150,429,895 bp (29.62%) number of C's = 95,998,351 bp (18.9%) number of T's = 154,448,920 bp (30.42%) number of G's = 106,833,389 bp (21.04%) number of N's = 87,385 bp (0.02%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,349,742 number of insertions = 20,638 mapped reads with insertion percentage = 0.19% number of deletions = 73,361 mapped reads with deletion percentage = 0.68% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.1641X std coverageData = 1.2474X There is a 7.04% of reference with a coverageData >= 1X There is a 3.03% of reference with a coverageData >= 2X There is a 1.73% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 28875678 0.11584997415111756 1.1138499654513392 chr2 243199373 42619036 0.17524319850939749 1.149587595853757 chr3 198022430 39410029 0.19901800518254423 1.602267079097685 chr4 191154276 32697726 0.1710541175652278 1.2407994820144201 chr5 180915260 31223158 0.17258443538704252 1.0030615597264498 chr6 171115067 28479374 0.16643405223924554 1.0853961241746177 chr7 159138663 26499832 0.16652038857458543 1.105818283484376 chr8 146364022 31818726 0.21739444957313347 1.268807996112393 chr9 141213431 19622554 0.13895671156095626 1.776781805428851 chr10 135534747 21680938 0.15996590158536983 1.1215043725987854 chr11 135006516 27482565 0.2035647301645796 1.294177001992744 chr12 133851895 26175965 0.19555916634575848 1.3494459423520195 chr13 115169878 19912748 0.17289892414403704 1.297635552248235 chr14 107349540 11053430 0.1029667197456086 0.8154392117653383 chr15 102531392 15103450 0.14730561738594167 0.9184134624914128 chr16 90354753 16597736 0.18369521745026518 1.1744495742827992 chr17 81195210 11080547 0.13646798869046586 2.180546468425085 chr18 78077248 19332283 0.24760456464859007 1.451771430666711 chr19 59128983 10347140 0.17499269351546262 1.2622016128361508 chr20 63025520 10627378 0.1686202351047639 1.0183373942252856 chr21 48129895 5889628 0.1223694337999283 0.9251617932897063 chr22 51304566 6765874 0.131876644273728 0.8573863518951621 chrMT 16571 19683 1.1877979602920765 2.968447148053516 chrX 155270560 23604636 0.15202261136947018 1.1434579886378406 chrY 59373566 987375 0.016629875321957248 0.4289796595699234