BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090210.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 = 26,410,121 number of mapped reads = 22,824,562 (86.42%) number of supplementary alignments = 1,230 (0%) number of secondary alignments = 0 number of mapped bases = 1,076,251,427 bp number of sequenced bases = 1,076,053,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,536,273 duplication rate = 12.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3599 >>>>>>> ACTG content number of A's = 314,475,046 bp (29.22%) number of C's = 219,406,565 bp (20.39%) number of T's = 310,900,714 bp (28.89%) number of G's = 231,102,269 bp (21.48%) number of N's = 169,393 bp (0.02%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,181,646 number of insertions = 39,291 mapped reads with insertion percentage = 0.17% number of deletions = 129,741 mapped reads with deletion percentage = 0.57% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.3477X std coverageData = 1.882X There is a 14.81% of reference with a coverageData >= 1X There is a 7.54% of reference with a coverageData >= 2X There is a 4.3% of reference with a coverageData >= 3X There is a 2.6% of reference with a coverageData >= 4X There is a 1.64% of reference with a coverageData >= 5X There is a 1.06% of reference with a coverageData >= 6X There is a 0.7% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.17% 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 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% 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% 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 90219830 0.3619643138221108 2.9931907202579477 chr2 243199373 102944474 0.4232925139983811 2.229929389297239 chr3 198022430 101639500 0.5132726631018516 1.4890510884615353 chr4 191154276 43897758 0.2296457025109917 0.9811907404521649 chr5 180915260 50940696 0.28157213493212235 1.0535406631512438 chr6 171115067 61735177 0.36078165460438383 1.3443746697694743 chr7 159138663 78934522 0.49601096623515056 2.9030628954468 chr8 146364022 94537000 0.6459032671294043 3.3064209283306014 chr9 141213431 35425258 0.2508632341069597 1.7802939353107279 chr10 135534747 34243860 0.25265742370847527 1.4853495952260654 chr11 135006516 46593401 0.3451196459287935 1.6307555607238275 chr12 133851895 39512742 0.2951974792736405 1.119235763075062 chr13 115169878 34324784 0.2980361236468445 1.0699788291545933 chr14 107349540 40059289 0.3731668435654219 1.2580205157411892 chr15 102531392 29721191 0.28987406120459186 1.0656582273835584 chr16 90354753 22024398 0.24375472533249026 1.039197878277109 chr17 81195210 22878840 0.2817757352927593 1.2073332186469021 chr18 78077248 39809255 0.5098701096637013 2.934017484753663 chr19 59128983 19088100 0.3228213818593836 2.041929477820704 chr20 63025520 27020973 0.4287306633884179 1.3982373277236197 chr21 48129895 15955097 0.33150076475338247 1.3122949771810604 chr22 51304566 8964073 0.17472271376391724 0.8260894497321253 chrMT 16571 335074 20.220505702733693 14.493501983437136 chrX 155270560 32801468 0.21125362077653356 1.103449733122752 chrY 59373566 2644667 0.044542835779814875 1.5182007657689434