BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472770.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 = 17,030,188 number of mapped reads = 16,829,339 (98.82%) number of supplementary alignments = 103,775 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,443,239 number of mapped paired reads (second in pair) = 8,386,100 number of mapped paired reads (both in pair) = 16,732,258 number of mapped paired reads (singletons) = 97,081 number of mapped bases = 1,658,867,086 bp number of sequenced bases = 1,658,641,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,551,633 duplication rate = 47.24% >>>>>>> Insert size mean insert size = 47,682.9976 std insert size = 2,141,776.8404 median insert size = 245 >>>>>>> Mapping quality mean mapping quality = 55.1211 >>>>>>> ACTG content number of A's = 451,976,476 bp (27.25%) number of C's = 380,512,491 bp (22.94%) number of T's = 449,557,591 bp (27.1%) number of G's = 376,276,058 bp (22.69%) number of N's = 319,361 bp (0.02%) GC percentage = 45.63% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,411,585 number of insertions = 94,326 mapped reads with insertion percentage = 0.56% number of deletions = 89,042 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.5359X std coverageData = 17.2219X There is a 4.88% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 204386940 0.8200057403267212 25.439988442508557 chr2 243199373 125866182 0.517543201067381 17.181293123248995 chr3 198022430 212672497 1.0739818564997914 23.352689290034853 chr4 191154276 63838191 0.33396161642756034 14.010054107141954 chr5 180915260 81399487 0.4499315701726875 13.07399927790453 chr6 171115067 133310755 0.7790708167153977 25.956955193939756 chr7 159138663 59538212 0.37412788870797536 10.18496960792363 chr8 146364022 69305205 0.47351257537866787 15.023014803896045 chr9 141213431 98658931 0.6986511856651936 18.363993830703105 chr10 135534747 40587750 0.29946379727996986 10.797866375550031 chr11 135006516 72942535 0.5402889961251944 14.40192752787336 chr12 133851895 82978900 0.6199307077423147 17.939428542775683 chr13 115169878 32564168 0.2827490014359484 11.306975941123312 chr14 107349540 39054356 0.36380552725237575 13.30522157202414 chr15 102531392 40574428 0.39572688138282563 13.137609509643964 chr16 90354753 55863104 0.6182641437800178 18.01962664446432 chr17 81195210 60932788 0.7504480621455379 15.51415202987111 chr18 78077248 24910326 0.31904718260561643 12.678740254816654 chr19 59128983 37653403 0.6368011267841356 17.29002153459381 chr20 63025520 26518275 0.420754561009572 10.483915099288621 chr21 48129895 10154243 0.21097579789027174 10.219761017056666 chr22 51304566 17481002 0.3407299459467214 11.406052798611412 chrMT 16571 6197 0.3739665681008992 1.2368316498909262 chrX 155270560 65701795 0.4231439301822573 19.63573641296249 chrY 59373566 1967416 0.033136227660639415 1.2578987698628246