BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548946.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 4,449,915 number of mapped reads = 3,793,076 (85.24%) number of secondary alignments = 0 number of mapped bases = 150,366,526 bp number of sequenced bases = 150,352,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,211 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1874 >>>>>>> ACTG content number of A's = 42,716,731 bp (28.41%) number of C's = 32,075,558 bp (21.33%) number of T's = 43,412,600 bp (28.87%) number of G's = 32,145,974 bp (21.38%) number of N's = 1,266 bp (0%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 338,312 number of insertions = 4,127 mapped reads with insertion percentage = 0.11% number of deletions = 10,709 mapped reads with deletion percentage = 0.28% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.7164X There is a 3.95% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 12205142 0.04896734841033756 0.7067065097414077 chr2 243199373 12942281 0.05321675315338909 0.3291293942258625 chr3 198022430 10336489 0.05219857669658937 0.27110078985989294 chr4 191154276 9625068 0.05035235518351679 0.27456114010472854 chr5 180915260 9327070 0.05155491029336055 0.26977942707397723 chr6 171115067 8838749 0.051653832447145054 0.27531762568293966 chr7 159138663 8533269 0.05362159540073552 0.5476490422422043 chr8 146364022 8060076 0.05506869714197933 2.846008915530258 chr9 141213431 6413972 0.045420410470729235 0.29792337395335045 chr10 135534747 7264157 0.053596270777706914 0.33410645709036507 chr11 135006516 7059905 0.05229306858048244 0.33611771663798334 chr12 133851895 6913332 0.05164911561394032 0.2729649650863377 chr13 115169878 4784586 0.041543727258268 0.23995766828548357 chr14 107349540 4639016 0.043214120898887876 0.2602585068992165 chr15 102531392 4483065 0.04372382850317686 0.24595647824326533 chr16 90354753 4408675 0.04879295060438049 0.27143613728799476 chr17 81195210 4088170 0.05034989132979643 0.27510359412173996 chr18 78077248 3924159 0.05025995537137784 0.4862684007510628 chr19 59128983 3014503 0.050981817157247575 0.5486375383594624 chr20 63025520 3372631 0.05351214872959398 0.27936589140270734 chr21 48129895 1986916 0.04128236722727112 0.26827536534550744 chr22 51304566 1889782 0.03683457725770451 0.3000206188053495 chrMT 16571 17714 1.0689759217910808 1.5479860212706575 chrX 155270560 4765282 0.03069018363816038 0.23290155882292665 chrY 59373566 1472517 0.02480088529632867 0.3181646322287618