BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472595.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,752,098 number of mapped reads = 10,035,844 (93.34%) number of supplementary alignments = 187,908 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,061,770 number of mapped paired reads (second in pair) = 4,974,074 number of mapped paired reads (both in pair) = 9,841,830 number of mapped paired reads (singletons) = 194,014 number of mapped bases = 827,306,081 bp number of sequenced bases = 826,948,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,875,340 duplication rate = 16.11% >>>>>>> Insert size mean insert size = 116,627.6923 std insert size = 3,263,241.0126 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 51.3555 >>>>>>> ACTG content number of A's = 215,908,124 bp (26.11%) number of C's = 166,219,282 bp (20.1%) number of T's = 245,012,702 bp (29.63%) number of G's = 199,261,826 bp (24.1%) number of N's = 546,274 bp (0.07%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 9,273,923 number of insertions = 72,006 mapped reads with insertion percentage = 0.7% number of deletions = 190,583 mapped reads with deletion percentage = 1.86% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.2672X std coverageData = 2.0788X There is a 12.99% of reference with a coverageData >= 1X There is a 6.67% of reference with a coverageData >= 2X There is a 2.85% of reference with a coverageData >= 3X There is a 1.53% of reference with a coverageData >= 4X There is a 0.8% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% 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 0.01% 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% 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 52141671 0.20919374559953455 2.960530492809951 chr2 243199373 77747526 0.31968637517827814 2.6762360823679887 chr3 198022430 41425607 0.20919653899813268 0.7603200595617022 chr4 191154276 37800148 0.19774680844701586 1.1404997362824194 chr5 180915260 36468463 0.20157759494693814 0.7640152964968817 chr6 171115067 50890589 0.29740565744569997 1.3142699238257516 chr7 159138663 73945221 0.4646590564858522 4.0400380583863145 chr8 146364022 38071903 0.2601179065713294 1.7950399516982867 chr9 141213431 26939184 0.19076927604712046 2.1901810655981673 chr10 135534747 43875644 0.3237224768641801 2.159390965043432 chr11 135006516 43040599 0.31880386425200397 2.236830571472086 chr12 133851895 39444627 0.29468859592910507 0.9382942311500351 chr13 115169878 36189739 0.3142292032296848 0.9741092198954103 chr14 107349540 19222311 0.1790628166641422 3.3848625081735824 chr15 102531392 23445129 0.22866293476245791 0.818834413670759 chr16 90354753 28724808 0.31791142188170224 1.3740397360631869 chr17 81195210 25613886 0.3154605548775599 1.6633882718130493 chr18 78077248 17456590 0.22358101043725312 3.442423590220139 chr19 59128983 13934275 0.2356589660945124 2.0535378768295067 chr20 63025520 28514102 0.4524215270258778 1.376474026091982 chr21 48129895 11976723 0.24884166067679972 1.098903388557805 chr22 51304566 7812796 0.1522826642759243 0.6632638168033059 chrMT 16571 248044 14.968559531712026 9.18693315360061 chrX 155270560 50463463 0.32500341983696074 1.3086746202192117 chrY 59373566 1913033 0.03222028132856295 0.8821971761321553