BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,160,262 number of mapped reads = 4,260,522 (82.56%) number of supplementary alignments = 24,579 (0.48%) number of secondary alignments = 0 number of mapped bases = 271,956,888 bp number of sequenced bases = 271,868,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 499,410 duplication rate = 9.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3223 >>>>>>> ACTG content number of A's = 79,931,096 bp (29.4%) number of C's = 56,055,902 bp (20.62%) number of T's = 76,278,532 bp (28.06%) number of G's = 58,981,891 bp (21.7%) number of N's = 620,610 bp (0.23%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,679,727 number of insertions = 18,346 mapped reads with insertion percentage = 0.43% number of deletions = 48,021 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0879X std coverageData = 0.5565X There is a 5.65% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 33366635 0.13386781090507294 0.745997735929634 chr2 243199373 19324387 0.07945903298031941 0.5153504723500696 chr3 198022430 15401892 0.07777852236234047 0.40688869275082706 chr4 191154276 17134201 0.08963545759237947 0.4851935262785459 chr5 180915260 20025282 0.11068873902621593 0.48823884551390656 chr6 171115067 17469195 0.1020903378426635 0.6445845231462939 chr7 159138663 18519629 0.11637416483761712 0.8757279424287984 chr8 146364022 13710342 0.09367289729165819 0.6303782737821159 chr9 141213431 8963780 0.06347682324919929 0.4328849022644852 chr10 135534747 12081833 0.08914196003184335 0.7036007557265088 chr11 135006516 11255500 0.0833700500796569 0.5218748351025909 chr12 133851895 10919116 0.08157610319973431 0.426284533091746 chr13 115169878 11273251 0.09788367579932662 0.46661908811988195 chr14 107349540 7766343 0.07234630907594015 0.4599490945388558 chr15 102531392 6442083 0.06283034760710164 0.36703647165147196 chr16 90354753 7258423 0.08033249783771751 0.44702436639617477 chr17 81195210 5162698 0.06358377544685209 0.38667547432588983 chr18 78077248 3858231 0.04941556085583344 0.6601659458802516 chr19 59128983 4707905 0.07962093648727224 0.6861924512877575 chr20 63025520 4532578 0.07191655062901504 0.4172303326565416 chr21 48129895 4199262 0.08724851778712586 0.5347828831191056 chr22 51304566 1808709 0.03525434753702039 0.27405346421443993 chrMT 16571 108754 6.56291110977008 5.5238055653411395 chrX 155270560 15924398 0.10255902986374237 0.4944893548158001 chrY 59373566 742461 0.012504908329070212 0.30312649816572673