BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006038.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 11,467,438 number of mapped reads = 8,434,324 (73.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,237,256 number of mapped paired reads (second in pair) = 4,197,068 number of mapped paired reads (both in pair) = 7,604,372 number of mapped paired reads (singletons) = 829,952 number of mapped bases = 324,985,221 bp number of sequenced bases = 324,945,509 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,104 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 64,643.8146 std insert size = 2,480,310.0461 median insert size = 70 >>>>>>> Mapping quality mean mapping quality = 46.2482 >>>>>>> ACTG content number of A's = 91,793,760 bp (28.25%) number of C's = 69,718,906 bp (21.46%) number of T's = 93,031,822 bp (28.63%) number of G's = 70,360,211 bp (21.65%) number of N's = 40,810 bp (0.01%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,983,944 number of insertions = 11,235 mapped reads with insertion percentage = 0.13% number of deletions = 30,581 mapped reads with deletion percentage = 0.36% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.105X std coverageData = 0.6452X There is a 7.38% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 26913198 0.10797645314592817 0.791126643581529 chr2 243199373 27802541 0.11431995344823524 0.5353637860971944 chr3 198022430 22563056 0.11394192061980049 0.4408219860218275 chr4 191154276 21063565 0.11019144034214542 0.4788739309336143 chr5 180915260 20068302 0.11092652991240208 0.4340992693502371 chr6 171115067 18552293 0.10841998501511267 0.5022470134321788 chr7 159138663 17646795 0.11088942603470284 0.6095189757780286 chr8 146364022 16759891 0.11450827034529018 1.477052498557398 chr9 141213431 13309981 0.09425435601801928 0.4530517921080677 chr10 135534747 15092432 0.11135470670115317 0.6272894854684633 chr11 135006516 14704149 0.10891436528885762 0.471207565794949 chr12 133851895 14977163 0.11189354472717775 0.43914016907974024 chr13 115169878 10520816 0.09135041369063532 0.39484556460538317 chr14 107349540 9967032 0.09284652733490986 0.42365064736716124 chr15 102531392 9296561 0.09067038707520912 0.39360317842088743 chr16 90354753 9105234 0.10077205346352948 0.4612622926782916 chr17 81195210 8650178 0.10653557026331972 0.4346585539375895 chr18 78077248 8515710 0.10906775300276977 0.6168187112269076 chr19 59128983 6326852 0.10700085946007223 1.8281444197268242 chr20 63025520 6809350 0.10804115539229188 0.44390944483317835 chr21 48129895 4055917 0.08427022331962286 0.4243777769982205 chr22 51304566 3624839 0.07065334106909704 0.4694151320588889 chrMT 16571 15833 0.9554643654577274 1.3309187776344757 chrX 155270560 17801056 0.11464540348150995 0.4633800885742653 chrY 59373566 842477 0.014189429012904497 0.3014233096157874