BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124913.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 = 4,411,482 number of mapped reads = 4,372,984 (99.13%) number of supplementary alignments = 17,398 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,188,107 number of mapped paired reads (second in pair) = 2,184,877 number of mapped paired reads (both in pair) = 4,358,772 number of mapped paired reads (singletons) = 14,212 number of mapped bases = 400,003,109 bp number of sequenced bases = 399,806,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,778 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 67,955.9266 std insert size = 2,521,869.123 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.5656 >>>>>>> ACTG content number of A's = 115,485,075 bp (28.89%) number of C's = 79,337,723 bp (19.84%) number of T's = 118,127,761 bp (29.55%) number of G's = 86,594,012 bp (21.66%) number of N's = 261,956 bp (0.07%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 3,291,800 number of insertions = 60,180 mapped reads with insertion percentage = 1.35% number of deletions = 117,780 mapped reads with deletion percentage = 2.64% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.1292X std coverageData = 1.3204X There is a 9% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 0.57% 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 0.03% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 35428012 0.14213810925670672 1.4711941441675067 chr2 243199373 35223702 0.144834674388737 1.754854624694356 chr3 198022430 31385698 0.1584956714246967 0.5235770286241384 chr4 191154276 17443664 0.09125437507869298 0.8599825158728696 chr5 180915260 17956543 0.09925388825685573 0.4003030839440147 chr6 171115067 23609309 0.13797329138760178 0.7486735820266678 chr7 159138663 20315630 0.12765992636245788 2.227746693020091 chr8 146364022 28812219 0.1968531515210753 0.7933436912006574 chr9 141213431 22544831 0.15965075588312844 2.2590079178056444 chr10 135534747 21799059 0.160837419794645 2.7861615247598213 chr11 135006516 15971594 0.11830239364150394 0.6715629756504538 chr12 133851895 15389752 0.11497597400470123 0.43171797017882285 chr13 115169878 15990309 0.13884106918998387 0.4743087051085857 chr14 107349540 12924986 0.12040094442882568 0.5127365169909287 chr15 102531392 7872638 0.07678270865570615 0.34651226963284215 chr16 90354753 12139866 0.13435780185243826 1.938030027282607 chr17 81195210 8981264 0.11061322459785497 0.8317270484711903 chr18 78077248 8161509 0.10453120734993118 2.2366184343189928 chr19 59128983 5486288 0.09278508984333453 0.8916673205517189 chr20 63025520 9975432 0.15827607610377512 0.5559764959561984 chr21 48129895 6916239 0.14369944085687283 0.5977921155664903 chr22 51304566 4934905 0.09618841722586641 0.3980574922789467 chrMT 16571 135302 8.164987025526523 5.074454726366998 chrX 155270560 19793192 0.12747549825285617 0.6042691537735506 chrY 59373566 811166 0.013662073118532243 0.8446929306876634