BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153325.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 171,484,808 number of mapped reads = 168,112,031 (98.03%) number of supplementary alignments = 922,476 (0.54%) number of secondary alignments = 0 number of mapped bases = 16,183,921,444 bp number of sequenced bases = 16,181,382,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,807,975 duplication rate = 36.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6505 >>>>>>> ACTG content number of A's = 4,164,763,884 bp (25.74%) number of C's = 3,926,474,753 bp (24.27%) number of T's = 4,221,651,174 bp (26.09%) number of G's = 3,864,265,607 bp (23.88%) number of N's = 4,227,139 bp (0.03%) GC percentage = 48.15% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 60,416,044 number of insertions = 904,645 mapped reads with insertion percentage = 0.53% number of deletions = 1,157,528 mapped reads with deletion percentage = 0.68% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 5.2279X std coverageData = 36.6239X There is a 58.52% of reference with a coverageData >= 1X There is a 42.1% of reference with a coverageData >= 2X There is a 28.56% of reference with a coverageData >= 3X There is a 20.77% of reference with a coverageData >= 4X There is a 15.22% of reference with a coverageData >= 5X There is a 11.78% of reference with a coverageData >= 6X There is a 9.4% of reference with a coverageData >= 7X There is a 7.83% of reference with a coverageData >= 8X There is a 6.72% of reference with a coverageData >= 9X There is a 5.94% of reference with a coverageData >= 10X There is a 5.37% of reference with a coverageData >= 11X There is a 4.93% of reference with a coverageData >= 12X There is a 4.6% of reference with a coverageData >= 13X There is a 4.33% of reference with a coverageData >= 14X There is a 4.11% of reference with a coverageData >= 15X There is a 3.92% of reference with a coverageData >= 16X There is a 3.76% of reference with a coverageData >= 17X There is a 3.63% of reference with a coverageData >= 18X There is a 3.5% of reference with a coverageData >= 19X There is a 3.4% of reference with a coverageData >= 20X There is a 3.3% of reference with a coverageData >= 21X There is a 3.2% of reference with a coverageData >= 22X There is a 3.12% of reference with a coverageData >= 23X There is a 3.04% of reference with a coverageData >= 24X There is a 2.97% of reference with a coverageData >= 25X There is a 2.9% of reference with a coverageData >= 26X There is a 2.83% of reference with a coverageData >= 27X There is a 2.77% of reference with a coverageData >= 28X There is a 2.71% of reference with a coverageData >= 29X There is a 2.66% of reference with a coverageData >= 30X There is a 2.6% of reference with a coverageData >= 31X There is a 2.55% of reference with a coverageData >= 32X There is a 2.5% of reference with a coverageData >= 33X There is a 2.45% of reference with a coverageData >= 34X There is a 2.41% of reference with a coverageData >= 35X There is a 2.36% of reference with a coverageData >= 36X There is a 2.32% of reference with a coverageData >= 37X There is a 2.28% of reference with a coverageData >= 38X There is a 2.24% of reference with a coverageData >= 39X There is a 2.2% of reference with a coverageData >= 40X There is a 2.16% of reference with a coverageData >= 41X There is a 2.12% of reference with a coverageData >= 42X There is a 2.09% of reference with a coverageData >= 43X There is a 2.05% of reference with a coverageData >= 44X There is a 2.02% of reference with a coverageData >= 45X There is a 1.99% of reference with a coverageData >= 46X There is a 1.95% of reference with a coverageData >= 47X There is a 1.92% of reference with a coverageData >= 48X There is a 1.89% of reference with a coverageData >= 49X There is a 1.86% of reference with a coverageData >= 50X There is a 1.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1713468333 6.874479694877069 41.653197109653135 chr2 243199373 1005913943 4.136169968661885 21.827769028096544 chr3 198022430 824989963 4.16614402216961 22.209745287857263 chr4 191154276 651477248 3.408122808615592 27.979926064149897 chr5 180915260 994028706 5.494443674900614 64.47623678341463 chr6 171115067 622214051 3.6362318170380634 20.89341617190181 chr7 159138663 911972251 5.730676843753551 41.46720789988619 chr8 146364022 858410808 5.864903111230436 68.62987926963324 chr9 141213431 548405783 3.8835242449423952 21.71725052487883 chr10 135534747 743507436 5.485733012804459 26.61204998085062 chr11 135006516 789236255 5.845912318780228 27.976109316993274 chr12 133851895 734309071 5.485981883185143 27.902674971238106 chr13 115169878 256851347 2.2301955290774904 13.227348033000197 chr14 107349540 434941168 4.051635135092335 23.246818347007853 chr15 102531392 756900261 7.38213191331685 39.48642169324577 chr16 90354753 731174179 8.092260282090528 43.34184248209972 chr17 81195210 713695022 8.789866077075237 48.577862359020564 chr18 78077248 250526253 3.208697276317936 21.99120496832964 chr19 59128983 829958064 14.036400118703208 59.3722786957803 chr20 63025520 412922181 6.551666388472479 31.91975199120989 chr21 48129895 198297234 4.120042937970258 35.07125484819039 chr22 51304566 316081800 6.160890241231161 32.43386487296993 chrMT 16571 42580 2.5695492124796333 2.283761460125332 chrX 155270560 865112368 5.571644540987036 30.87385551081637 chrY 59373566 19485139 0.3281786881387586 13.434395874651907