BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975330.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,585,008 number of mapped reads = 2,386,901 (66.58%) number of supplementary alignments = 13,520 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,193,048 number of mapped paired reads (second in pair) = 1,193,853 number of mapped paired reads (both in pair) = 2,363,068 number of mapped paired reads (singletons) = 23,833 number of mapped bases = 217,777,575 bp number of sequenced bases = 217,656,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,154 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 60,800.6193 std insert size = 2,346,963.1747 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.5206 >>>>>>> ACTG content number of A's = 63,967,512 bp (29.39%) number of C's = 42,611,919 bp (19.58%) number of T's = 65,444,857 bp (30.07%) number of G's = 45,627,415 bp (20.96%) number of N's = 4,962 bp (0%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,674,756 number of insertions = 37,069 mapped reads with insertion percentage = 1.51% number of deletions = 67,042 mapped reads with deletion percentage = 2.75% homopolymer indels = 44.71% >>>>>>> Coverage mean coverageData = 0.0703X std coverageData = 0.9155X There is a 5.09% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 19956187 0.0800647433492252 0.9870676596546688 chr2 243199373 20668105 0.08498420347489959 1.217161057130637 chr3 198022430 16178019 0.08169791169616493 0.4317813418086925 chr4 191154276 10829242 0.05665184282877355 0.6972373814725281 chr5 180915260 9547482 0.05277322653710914 0.28239928651229446 chr6 171115067 13419714 0.07842508690365647 0.7287588802936796 chr7 159138663 12099866 0.07603347779791263 1.1433820316758625 chr8 146364022 17899426 0.1222938926890107 0.6351042816474931 chr9 141213431 6644461 0.04705261357186343 1.2714377645797539 chr10 135534747 8927409 0.06586804636895069 2.1397388522017575 chr11 135006516 8219011 0.06087862455468446 0.47080207926523315 chr12 133851895 9708924 0.0725348266455249 0.3360334815219503 chr13 115169878 4846676 0.042082843918615595 0.24648370107237513 chr14 107349540 8712535 0.08116043161433202 0.37556268509217816 chr15 102531392 4045625 0.0394574278285425 0.24228921790274568 chr16 90354753 5480454 0.06065485011065218 1.2750042662117367 chr17 81195210 5834650 0.07185953457106645 1.2639564964974508 chr18 78077248 8319218 0.10655111717052322 1.5223356985195238 chr19 59128983 3370848 0.05700838791697128 0.5117139056550295 chr20 63025520 5564350 0.0882872525288169 0.40143820396806423 chr21 48129895 3558777 0.0739410921216429 0.40139406069052325 chr22 51304566 1883536 0.036712833707627505 0.24368655919738447 chrMT 16571 89998 5.4310542514030535 6.950366818875113 chrX 155270560 9573758 0.06165855265801837 0.4190016641357978 chrY 59373566 2399304 0.04041030649902349 0.8540910516208949