BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085103.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,425,956 number of mapped reads = 1,076,534 (75.5%) number of supplementary alignments = 5,297 (0.37%) number of secondary alignments = 0 number of mapped bases = 68,059,143 bp number of sequenced bases = 68,037,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,505 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3075 >>>>>>> ACTG content number of A's = 20,300,482 bp (29.84%) number of C's = 12,649,618 bp (18.59%) number of T's = 19,873,233 bp (29.21%) number of G's = 15,212,285 bp (22.36%) number of N's = 1,517 bp (0%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 622,806 number of insertions = 5,212 mapped reads with insertion percentage = 0.48% number of deletions = 13,599 mapped reads with deletion percentage = 1.25% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.1841X There is a 2.04% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 5446926 0.021853209344661974 0.24602319068015233 chr2 243199373 7203767 0.029620828833304597 0.2117086036000888 chr3 198022430 4605361 0.023256764397851293 0.16109376167677797 chr4 191154276 4846626 0.02535452568165412 0.17176489349875063 chr5 180915260 3049532 0.016856134745073467 0.13754251690234914 chr6 171115067 5146930 0.03007876565305614 0.20516837011071998 chr7 159138663 5685377 0.035725931667529465 0.23368480057734123 chr8 146364022 4032034 0.027547985802139272 0.24357821944033003 chr9 141213431 2373752 0.016809675844502353 0.15801180261276845 chr10 135534747 4340538 0.03202527835906168 0.2398615089992073 chr11 135006516 2934204 0.021733795426585188 0.18100143138976 chr12 133851895 2821287 0.021077676935391913 0.1540262790339539 chr13 115169878 1324616 0.011501410116975204 0.11202607085435558 chr14 107349540 1713689 0.015963636173941687 0.13815563648115134 chr15 102531392 1154046 0.011255538206289056 0.1107247328938735 chr16 90354753 1588470 0.017580370121757734 0.14486810142512513 chr17 81195210 1273326 0.015682279779804745 0.14112274034390665 chr18 78077248 1826771 0.02339696962679832 0.22630398321483505 chr19 59128983 1090386 0.0184408042330104 0.19147504849009025 chr20 63025520 1444455 0.02291857330173555 0.16131391996729097 chr21 48129895 697509 0.014492219440744676 0.1330257142104248 chr22 51304566 390133 0.007604254950719201 0.09073583437667508 chrMT 16571 3628 0.21893669663870619 0.5277695362545978 chrX 155270560 2930562 0.01887390629620966 0.14985938519398853 chrY 59373566 135218 0.002277410792540236 0.06252430333758513