BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089705.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 26,893,657 number of mapped reads = 25,331,493 (94.19%) number of supplementary alignments = 201,941 (0.75%) number of secondary alignments = 0 number of mapped bases = 1,666,916,200 bp number of sequenced bases = 1,666,333,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,159,888 duplication rate = 15.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.552 >>>>>>> ACTG content number of A's = 433,556,401 bp (26.02%) number of C's = 320,979,146 bp (19.26%) number of T's = 509,730,049 bp (30.59%) number of G's = 401,960,384 bp (24.12%) number of N's = 107,909 bp (0.01%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,253,583 number of insertions = 102,650 mapped reads with insertion percentage = 0.4% number of deletions = 326,179 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.5385X std coverageData = 2.9845X There is a 16.37% of reference with a coverageData >= 1X There is a 10.2% of reference with a coverageData >= 2X There is a 6.86% of reference with a coverageData >= 3X There is a 4.79% of reference with a coverageData >= 4X There is a 3.42% of reference with a coverageData >= 5X There is a 2.5% of reference with a coverageData >= 6X There is a 1.86% of reference with a coverageData >= 7X There is a 1.4% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.84% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129887665 0.5211127036670452 4.954023591757815 chr2 243199373 144861022 0.5956471853239523 3.677568626845093 chr3 198022430 113578569 0.5735641613932321 1.9378399921709009 chr4 191154276 106188263 0.5555107906662784 2.2784588391761362 chr5 180915260 101110595 0.5588837282161825 1.8952175449003408 chr6 171115067 97953937 0.5724448391210343 2.4076128038984095 chr7 159138663 89018225 0.5593752223493293 3.1955528525476704 chr8 146364022 82360632 0.5627109099256646 3.420639090770611 chr9 141213431 69999197 0.4956978702684449 3.1383386067268666 chr10 135534747 80891647 0.5968332755289683 3.614873434600875 chr11 135006516 73616219 0.5452790071258486 2.979258312650863 chr12 133851895 74091545 0.5535337770152601 2.0297771663322255 chr13 115169878 51996746 0.4514786930659074 1.7338361627729693 chr14 107349540 52231634 0.4865566634007002 1.9225287171208254 chr15 102531392 48453405 0.4725714150062451 1.8729182107206142 chr16 90354753 50789977 0.5621173797022055 2.240055517520599 chr17 81195210 45251825 0.5573213616911638 2.634898448956595 chr18 78077248 43382107 0.5556305852378404 4.914888708211978 chr19 59128983 33768958 0.5711066939879551 3.863614018519692 chr20 63025520 36515876 0.5793823835170261 2.1979323488483513 chr21 48129895 22323653 0.46382093707040084 2.267471982225032 chr22 51304566 20051757 0.39083766930218256 1.692908449807947 chrMT 16571 8967 0.5411260636050932 1.3114208935914642 chrX 155270560 94241486 0.6069501262827931 2.2454666387996918 chrY 59373566 4342293 0.07313512211814935 1.59930250302115