BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 432,218 number of mapped reads = 397,070 (91.87%) number of supplementary alignments = 9,036 (2.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 199,306 number of mapped paired reads (second in pair) = 197,764 number of mapped paired reads (both in pair) = 394,358 number of mapped paired reads (singletons) = 2,712 number of mapped bases = 53,394,737 bp number of sequenced bases = 52,116,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 383,904 duplication rate = 46.4% >>>>>>> Insert size mean insert size = 236,180.8937 std insert size = 4,679,708.6962 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 41.2577 >>>>>>> ACTG content number of A's = 15,088,403 bp (28.95%) number of C's = 11,073,666 bp (21.25%) number of T's = 14,477,976 bp (27.78%) number of G's = 11,475,771 bp (22.02%) number of N's = 489 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0406 number of mismatches = 2,108,693 number of insertions = 23,957 mapped reads with insertion percentage = 5.96% number of deletions = 167,497 mapped reads with deletion percentage = 40.74% homopolymer indels = 28.83% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 9.1066X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 350019 0.0014042853678587223 0.5301306047536057 chr2 243199373 1276076 0.005247036553831905 1.958015618953924 chr3 198022430 460992 0.002327978704230627 0.7613586569696008 chr4 191154276 1035285 0.005415965688363675 2.5497498967113508 chr5 180915260 1453286 0.0080329652678276 3.562484570584501 chr6 171115067 916687 0.005357137837546474 2.5150600873859834 chr7 159138663 3350132 0.021051653550715078 9.05692866761935 chr8 146364022 303950 0.0020766715470554643 0.627906007815974 chr9 141213431 1006294 0.00712605021260336 2.517785999577837 chr10 135534747 669174 0.0049372874101428765 2.207437399256657 chr11 135006516 831411 0.0061583027592534865 2.281812461283047 chr12 133851895 2634659 0.019683389615066712 7.297719857221201 chr13 115169878 561216 0.004872940822252152 1.8619709674050005 chr14 107349540 536191 0.004994814137070359 2.948887881841153 chr15 102531392 425142 0.0041464569212129685 1.1352941990058691 chr16 90354753 278398 0.0030811660787783903 0.7255187029819798 chr17 81195210 1043052 0.012846225781052848 4.327564193666599 chr18 78077248 590233 0.00755960302289343 3.067830993986159 chr19 59128983 177099 0.0029951301546992616 0.8290191451828488 chr20 63025520 97180 0.0015419150845562243 0.5002423889093238 chr21 48129895 118880 0.0024699825337246217 0.5566043664216048 chr22 51304566 191259 0.0037279138079055188 0.9286162291577059 chrMT 16571 8603517 519.1911773580351 2833.6229611330905 chrX 155270560 26401207 0.17003356592518246 23.678931358687482 chrY 59373566 83398 0.0014046318188131062 0.6584695410257551