BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927037.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 = 35,119,132 number of mapped reads = 34,258,867 (97.55%) number of supplementary alignments = 842,739 (2.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,169,870 number of mapped paired reads (second in pair) = 17,088,997 number of mapped paired reads (both in pair) = 33,771,800 number of mapped paired reads (singletons) = 487,067 number of mapped bases = 3,117,479,523 bp number of sequenced bases = 3,115,178,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,667,872 duplication rate = 8.28% >>>>>>> Insert size mean insert size = 232,113.7638 std insert size = 4,768,457.2594 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 52.9302 >>>>>>> ACTG content number of A's = 875,722,155 bp (28.11%) number of C's = 618,912,400 bp (19.87%) number of T's = 896,274,395 bp (28.77%) number of G's = 723,881,213 bp (23.24%) number of N's = 388,483 bp (0.01%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 32,228,844 number of insertions = 516,082 mapped reads with insertion percentage = 1.48% number of deletions = 1,590,815 mapped reads with deletion percentage = 4.53% homopolymer indels = 52.16% >>>>>>> Coverage mean coverageData = 1.007X std coverageData = 3.7897X There is a 35.94% of reference with a coverageData >= 1X There is a 21.08% of reference with a coverageData >= 2X There is a 12.89% of reference with a coverageData >= 3X There is a 8.4% of reference with a coverageData >= 4X There is a 5.66% of reference with a coverageData >= 5X There is a 3.93% of reference with a coverageData >= 6X There is a 2.79% of reference with a coverageData >= 7X There is a 2.02% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.11% of reference with a coverageData >= 10X There is a 0.84% of reference with a coverageData >= 11X There is a 0.64% of reference with a coverageData >= 12X There is a 0.5% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 268684891 1.077970798716686 3.7511191697162416 chr2 243199373 267245532 1.0988742639562643 4.800724232898514 chr3 198022430 199325306 1.0065794364810088 2.0745161411636253 chr4 191154276 169590766 0.8871931591004535 2.499536639679248 chr5 180915260 178677083 0.9876285892080082 2.0355138930140506 chr6 171115067 171408442 1.001714489583784 2.071708571338119 chr7 159138663 160572962 1.009012888338769 2.4271666516884474 chr8 146364022 151159022 1.0327607832476755 2.3396754109162408 chr9 141213431 139140482 0.985320454397854 4.118706242226592 chr10 135534747 156717295 1.1562886895712432 5.0990517197259235 chr11 135006516 148944308 1.1032379207533953 2.8988928125005984 chr12 133851895 137694662 1.0287090967221644 2.1359726915242474 chr13 115169878 84152648 0.7306827919015422 1.7201629349825598 chr14 107349540 96744905 0.9012139688721535 2.0620675787353955 chr15 102531392 98082531 0.9566097668897346 2.1317085529686706 chr16 90354753 104600224 1.1576615565536437 3.806237642831394 chr17 81195210 95671008 1.1782838913773361 2.756987337008143 chr18 78077248 81107371 1.0388092956350101 3.8028605022002773 chr19 59128983 64336806 1.0880756396571205 2.757121009225102 chr20 63025520 77854872 1.2352912280612678 2.5525457058988366 chr21 48129895 40495222 0.8413735787289791 2.8288216033311375 chr22 51304566 48403892 0.9434616794146549 2.3027512861184825 chrMT 16571 12417664 749.3611731337879 594.0908852422798 chrX 155270560 159136581 1.0248986092405412 2.259559083927505 chrY 59373566 5315048 0.08951875991413417 3.134653052970306