BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124949.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 7,113,326 number of mapped reads = 6,955,990 (97.79%) number of supplementary alignments = 6,625 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,512,095 number of mapped paired reads (second in pair) = 3,443,895 number of mapped paired reads (both in pair) = 6,867,056 number of mapped paired reads (singletons) = 88,934 number of mapped bases = 434,928,040 bp number of sequenced bases = 434,754,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 453,058 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 25,284.0701 std insert size = 1,514,759.9979 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 51.8374 >>>>>>> ACTG content number of A's = 119,314,645 bp (27.44%) number of C's = 78,564,603 bp (18.07%) number of T's = 129,628,731 bp (29.82%) number of G's = 107,242,994 bp (24.67%) number of N's = 3,280 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,766,127 number of insertions = 42,585 mapped reads with insertion percentage = 0.61% number of deletions = 120,253 mapped reads with deletion percentage = 1.71% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.1405X std coverageData = 1.006X There is a 10.46% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 39624633 0.15897506229282374 1.0512668058975845 chr2 243199373 31450534 0.129319963337241 0.9472084624918242 chr3 198022430 38712809 0.195497090910358 0.5637631508670174 chr4 191154276 30577479 0.1599623070948201 0.5912638799858299 chr5 180915260 14562239 0.08049204362307524 0.3462243217680968 chr6 171115067 48468627 0.283251661292924 2.0210432179291558 chr7 159138663 15126999 0.09505546116093737 0.9815858333608322 chr8 146364022 28117790 0.19210861805915663 0.6931606254958238 chr9 141213431 13894490 0.09839354444974856 0.8681578810656269 chr10 135534747 21851866 0.16122703943956157 2.1706969318865754 chr11 135006516 21371531 0.15829999642387632 1.0499304928723936 chr12 133851895 15682262 0.11716129980826943 0.4252733295677867 chr13 115169878 10471793 0.09092475551636861 0.35916398803746025 chr14 107349540 8514834 0.07931877491044675 0.42153360595521333 chr15 102531392 10232812 0.09980174657143054 0.4244730135435213 chr16 90354753 7882324 0.08723751367014417 0.7983838356239035 chr17 81195210 10144537 0.12494009190936263 1.3532093964958098 chr18 78077248 15093696 0.19331746938621608 1.2822717754171522 chr19 59128983 5960639 0.10080739930872817 1.0525810650540568 chr20 63025520 10977559 0.17417641298318523 0.5406797445911075 chr21 48129895 3460838 0.07190620299504082 0.40145424643668637 chr22 51304566 2392780 0.04663873387019783 0.2564627164660808 chrMT 16571 54179 3.269506970007845 2.8912932533140836 chrX 155270560 29464125 0.1897598939554285 0.9423157345714046 chrY 59373566 836665 0.014091540332948842 0.5383424777343846