BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472789.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 = 12,183,632 number of mapped reads = 12,069,189 (99.06%) number of supplementary alignments = 42,553 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,054,747 number of mapped paired reads (second in pair) = 6,014,442 number of mapped paired reads (both in pair) = 12,003,412 number of mapped paired reads (singletons) = 65,777 number of mapped bases = 1,187,071,791 bp number of sequenced bases = 1,186,902,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,284,163 duplication rate = 46.56% >>>>>>> Insert size mean insert size = 23,044.546 std insert size = 1,489,053.6589 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 55.1025 >>>>>>> ACTG content number of A's = 326,071,404 bp (27.47%) number of C's = 269,027,247 bp (22.67%) number of T's = 324,172,571 bp (27.31%) number of G's = 267,401,891 bp (22.53%) number of N's = 229,817 bp (0.02%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 7,281,957 number of insertions = 69,767 mapped reads with insertion percentage = 0.57% number of deletions = 67,993 mapped reads with deletion percentage = 0.56% homopolymer indels = 44.31% >>>>>>> Coverage mean coverageData = 0.3835X std coverageData = 13.8873X There is a 3.34% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 128622472 0.5160367163137379 16.01845303871818 chr2 243199373 71925209 0.2957458652658615 11.945030841951608 chr3 198022430 114022744 0.5758072153745412 12.528231624154177 chr4 191154276 36921421 0.19314985661110715 7.482106737774104 chr5 180915260 70225575 0.38816833361652303 16.108617514624775 chr6 171115067 99889065 0.5837537672822231 21.93335720037507 chr7 159138663 43188234 0.27138743775923263 8.4466456370537 chr8 146364022 73720692 0.5036804194954413 17.90562173811862 chr9 141213431 66208211 0.46885208107435616 13.006674787796134 chr10 135534747 45634050 0.33669631596390553 15.04023180967993 chr11 135006516 60743062 0.44992689093613825 17.000884685892547 chr12 133851895 48038731 0.35889466488315314 11.872062923458204 chr13 115169878 22648323 0.19665144561497236 9.459421056925974 chr14 107349540 22104441 0.20591090562661005 7.016693786223323 chr15 102531392 29675849 0.28943183566648545 10.997458869101436 chr16 90354753 55796301 0.6175248024860408 22.928607122781006 chr17 81195210 43707219 0.5382979981208251 11.591810484738971 chr18 78077248 21520049 0.2756250963148701 13.263397288948356 chr19 59128983 23958891 0.4051970756879076 9.28831834373727 chr20 63025520 21821785 0.34623728610251847 10.666271641698806 chr21 48129895 3013401 0.06260975636867688 2.3382393587925328 chr22 51304566 22144688 0.43163191361954023 20.35477659995448 chrMT 16571 2271 0.13704664775813166 0.49727803311104535 chrX 155270560 59167564 0.3810610588381983 11.936483227342194 chrY 59373566 2371543 0.03994274152238052 2.8806659725452537