BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927032.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 20,823,768 number of mapped reads = 20,181,443 (96.92%) number of supplementary alignments = 846,989 (4.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,125,522 number of mapped paired reads (second in pair) = 10,055,921 number of mapped paired reads (both in pair) = 19,831,554 number of mapped paired reads (singletons) = 349,889 number of mapped bases = 1,799,179,474 bp number of sequenced bases = 1,797,815,945 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,839,423 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 433,794.8877 std insert size = 6,446,937.8006 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.0608 >>>>>>> ACTG content number of A's = 510,580,266 bp (28.4%) number of C's = 348,284,487 bp (19.37%) number of T's = 524,665,341 bp (29.18%) number of G's = 414,101,797 bp (23.03%) number of N's = 184,054 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 19,878,558 number of insertions = 314,415 mapped reads with insertion percentage = 1.53% number of deletions = 923,911 mapped reads with deletion percentage = 4.46% homopolymer indels = 51.15% >>>>>>> Coverage mean coverageData = 0.5812X std coverageData = 2.4183X There is a 28.12% of reference with a coverageData >= 1X There is a 13.47% of reference with a coverageData >= 2X There is a 6.61% of reference with a coverageData >= 3X There is a 3.58% of reference with a coverageData >= 4X There is a 2.02% of reference with a coverageData >= 5X There is a 1.2% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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% 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 145390095 0.5833088576336988 2.8612181658425735 chr2 243199373 155748441 0.6404146486019107 3.974124385968795 chr3 198022430 123261560 0.6224626169873787 1.3669391097547166 chr4 191154276 111310650 0.5823079259812111 1.7384576366976356 chr5 180915260 109920112 0.6075778903338502 1.2983274294489349 chr6 171115067 104948777 0.6133228291346197 1.3416134267021627 chr7 159138663 92945289 0.584052217404893 1.7908519676787586 chr8 146364022 91932672 0.6281097686697896 1.6265837801965524 chr9 141213431 79663986 0.5641388742973039 2.9315650836388842 chr10 135534747 88089435 0.6499398637605455 5.412935944156849 chr11 135006516 84461226 0.6256085150734503 1.8653635975948855 chr12 133851895 80667117 0.6026595066136344 1.3186629312958182 chr13 115169878 54519805 0.473385975107137 1.135200364394613 chr14 107349540 54419286 0.5069354372641001 1.2595695769912172 chr15 102531392 51577065 0.5030368162757411 1.2070339733308038 chr16 90354753 56280343 0.6228819307380542 3.7173627569155054 chr17 81195210 45124028 0.5557474141639636 1.5383082958038408 chr18 78077248 47870290 0.6131144632556721 2.996518112382485 chr19 59128983 28427866 0.48077718502278316 1.7691421867155983 chr20 63025520 40628477 0.6446353318465282 1.4394000814018715 chr21 48129895 23334483 0.48482306059466784 1.710838405051787 chr22 51304566 21169717 0.4126283223992188 1.1680500421236215 chrMT 16571 122807 7.410958904109589 7.26910564640582 chrX 155270560 103841183 0.6687757357222129 1.5244166867494902 chrY 59373566 3524764 0.05936588009552938 2.43584147439888