BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549015.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,730,820 number of mapped reads = 6,756,445 (87.4%) number of secondary alignments = 0 number of mapped bases = 267,322,839 bp number of sequenced bases = 267,293,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 238,676 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3036 >>>>>>> ACTG content number of A's = 77,942,629 bp (29.16%) number of C's = 55,737,752 bp (20.85%) number of T's = 78,252,868 bp (29.28%) number of G's = 55,351,797 bp (20.71%) number of N's = 8,895 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 711,520 number of insertions = 8,729 mapped reads with insertion percentage = 0.13% number of deletions = 21,926 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.12% >>>>>>> Coverage mean coverageData = 0.0864X std coverageData = 0.8899X There is a 7.1% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% 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 21307685 0.08548698861616878 0.9733014765601463 chr2 243199373 22484318 0.09245220381386428 0.5474754065849617 chr3 198022430 17985018 0.09082313554075667 0.3525934854312872 chr4 191154276 17462522 0.09135302837797885 0.3618456174006452 chr5 180915260 16613130 0.0918282404701516 0.36216591275995974 chr6 171115067 15585256 0.09108055925899267 0.40383377991265146 chr7 159138663 14864367 0.09340512682326607 0.7856547956680388 chr8 146364022 13831252 0.09449898828278988 3.274968976462579 chr9 141213431 11120684 0.0787508944528088 0.5296933290133549 chr10 135534747 12245527 0.09034972411908512 0.47839564662736306 chr11 135006516 12102170 0.08964137701323986 0.5776779295486681 chr12 133851895 12088438 0.09031204227627856 0.3692787242026424 chr13 115169878 8742313 0.07590798177280347 0.31848044466724973 chr14 107349540 8364445 0.07791784669035377 0.4078513825513523 chr15 102531392 7607146 0.0741933358322103 0.31570999048195886 chr16 90354753 7481749 0.08280415530547684 0.37104902536046214 chr17 81195210 7111762 0.08758844271724896 0.3761340198708417 chr18 78077248 7076195 0.09063069179897325 0.9532862173222397 chr19 59128983 5364558 0.09072637017957844 0.9142374409969751 chr20 63025520 5329641 0.08456322137445275 0.35739468554942005 chr21 48129895 3378284 0.07019096966656586 0.35422846027562827 chr22 51304566 2962991 0.05775296880983264 0.33193802538535533 chrMT 16571 22732 1.3717940981232273 1.7388376197426325 chrX 155270560 15374447 0.09901714143363687 0.45884264309838635 chrY 59373566 816209 0.013747009906731895 0.1921374181422725