BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006021.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 8,777,998 number of mapped reads = 6,445,306 (73.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,247,568 number of mapped paired reads (second in pair) = 3,197,738 number of mapped paired reads (both in pair) = 5,742,188 number of mapped paired reads (singletons) = 703,118 number of mapped bases = 249,028,659 bp number of sequenced bases = 249,000,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,724 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 65,943.7505 std insert size = 2,451,003.8923 median insert size = 90 >>>>>>> Mapping quality mean mapping quality = 47.249 >>>>>>> ACTG content number of A's = 72,743,591 bp (29.21%) number of C's = 51,310,191 bp (20.61%) number of T's = 72,791,186 bp (29.23%) number of G's = 52,123,222 bp (20.93%) number of N's = 32,098 bp (0.01%) GC percentage = 41.54% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,528,791 number of insertions = 7,607 mapped reads with insertion percentage = 0.12% number of deletions = 22,382 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 0.0804X std coverageData = 0.4531X There is a 6.26% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20090731 0.08060453739050062 0.6142419358791992 chr2 243199373 21439261 0.0881550833603506 0.44358108147373915 chr3 198022430 17704785 0.08940797767202432 0.3643774384180119 chr4 191154276 16989121 0.08887648948015163 0.38792629584528554 chr5 180915260 14486299 0.08007228909269455 0.3429582673408456 chr6 171115067 15401719 0.09000796522494423 0.46850889926478057 chr7 159138663 13340183 0.08382741659705913 0.4893512296454577 chr8 146364022 12957873 0.08853181829069988 0.8491907926095532 chr9 141213431 10259176 0.0726501433139175 0.375379376462433 chr10 135534747 11195762 0.08260436712955978 0.5018852126761341 chr11 135006516 11358834 0.08413545017338274 0.4052565599342757 chr12 133851895 11159474 0.08337180433642721 0.3526169733451351 chr13 115169878 8316137 0.0722075697605584 0.3262474995597014 chr14 107349540 7720162 0.07191611626840692 0.34343129880447454 chr15 102531392 7184536 0.07007157378688471 0.322153735005097 chr16 90354753 6703285 0.07418851557261189 0.3816506978291044 chr17 81195210 6242290 0.07688002777503747 0.35695974907900385 chr18 78077248 6229695 0.07978886499688104 0.5385721006041547 chr19 59128983 4420416 0.0747588707893048 0.5139717067580439 chr20 63025520 4968054 0.07882606918594245 0.35231759602766344 chr21 48129895 3391877 0.07047339288814156 0.352133557444545 chr22 51304566 2608922 0.050851653242715275 0.2774777769341529 chrMT 16571 17186 1.0371130287852273 1.279534330822495 chrX 155270560 14240243 0.09171244696998582 0.39967929235233557 chrY 59373566 602638 0.010149937768602277 0.21705924785150824