BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038435.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,340,820 number of mapped reads = 14,943,533 (91.45%) number of supplementary alignments = 218,853 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,613,616 number of mapped paired reads (second in pair) = 7,329,917 number of mapped paired reads (both in pair) = 14,607,808 number of mapped paired reads (singletons) = 335,725 number of mapped bases = 2,017,446,592 bp number of sequenced bases = 2,016,045,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,770,762 duplication rate = 12.88% >>>>>>> Insert size mean insert size = 91,552.6812 std insert size = 2,958,585.8942 median insert size = 251 >>>>>>> Mapping quality mean mapping quality = 53.3529 >>>>>>> ACTG content number of A's = 577,809,552 bp (28.66%) number of C's = 401,371,277 bp (19.91%) number of T's = 588,396,988 bp (29.19%) number of G's = 448,311,371 bp (22.24%) number of N's = 155,935 bp (0.01%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 27,415,538 number of insertions = 348,044 mapped reads with insertion percentage = 2.21% number of deletions = 723,362 mapped reads with deletion percentage = 4.67% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.6517X std coverageData = 9.0835X There is a 25.81% of reference with a coverageData >= 1X There is a 14.5% of reference with a coverageData >= 2X There is a 8.02% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 2.91% of reference with a coverageData >= 5X There is a 1.82% of reference with a coverageData >= 6X There is a 1.15% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 173120155 0.6945625824539069 12.827594753987498 chr2 243199373 180982511 0.7441734276181707 9.628984470358048 chr3 198022430 148633023 0.750586804737221 1.7156298508972496 chr4 191154276 86236211 0.4511340933853868 7.9049562411526555 chr5 180915260 138907466 0.7678040315670441 1.629337556159358 chr6 171115067 120130835 0.7020470909204038 7.506091238150182 chr7 159138663 97691813 0.6138785582231516 9.126376435585094 chr8 146364022 129147973 0.8823751304128552 3.584502495316729 chr9 141213431 79693358 0.5643468715096938 14.202019398271407 chr10 135534747 124696252 0.9200316137381361 24.783036572593886 chr11 135006516 91334130 0.6765164579167423 7.926846086098582 chr12 133851895 83196104 0.6215534266436795 1.5912739421623556 chr13 115169878 68163856 0.5918548945584539 1.3889393475616838 chr14 107349540 64862635 0.6042190306544397 1.507566034221815 chr15 102531392 54297895 0.5295733720263937 1.3443169727606379 chr16 90354753 64507170 0.7139322266754468 9.891628330298188 chr17 81195210 48794651 0.6009547977029679 10.872086082361774 chr18 78077248 80345073 1.0290459136059713 9.671162502134624 chr19 59128983 25873360 0.4375749199001106 5.311306961332989 chr20 63025520 52646945 0.8353274197499679 2.988529621103853 chr21 48129895 19594417 0.40711530744041724 3.6319551540278003 chr22 51304566 11040595 0.21519712300070915 0.844139795372907 chrMT 16571 2047230 123.54293645525316 61.650420111576835 chrX 155270560 67413355 0.43416701144119013 2.050605144363067 chrY 59373566 4089579 0.06887878353137826 7.315530529857572