BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975193.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,164,196 number of mapped reads = 3,125,975 (98.79%) number of supplementary alignments = 49,093 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,564,919 number of mapped paired reads (second in pair) = 1,561,056 number of mapped paired reads (both in pair) = 3,114,022 number of mapped paired reads (singletons) = 11,953 number of mapped bases = 425,753,252 bp number of sequenced bases = 425,421,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 568,940 duplication rate = 14.9% >>>>>>> Insert size mean insert size = 90,500.0479 std insert size = 2,884,940.0443 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.4541 >>>>>>> ACTG content number of A's = 125,508,769 bp (29.5%) number of C's = 84,847,570 bp (19.94%) number of T's = 126,718,317 bp (29.79%) number of G's = 88,321,972 bp (20.76%) number of N's = 24,441 bp (0.01%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 5,405,429 number of insertions = 89,650 mapped reads with insertion percentage = 2.72% number of deletions = 165,751 mapped reads with deletion percentage = 5.11% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.1375X std coverageData = 3.3953X There is a 7.29% of reference with a coverageData >= 1X There is a 4.04% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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% 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 42805399 0.1717363785424631 4.314019217665738 chr2 243199373 29534866 0.12144301868738781 1.95157039275072 chr3 198022430 31573991 0.15944653845526488 0.8102772895677912 chr4 191154276 24045055 0.12578873726057793 1.8609292734428156 chr5 180915260 36724521 0.2029929426627693 0.664268369874791 chr6 171115067 20430294 0.11939506180364584 1.1333354337849157 chr7 159138663 17868927 0.11228526533492367 1.3026275207496365 chr8 146364022 27499493 0.18788423974848137 0.9847880848587536 chr9 141213431 14826253 0.10499180492257851 2.801126750697302 chr10 135534747 26031027 0.19206164895855082 13.202501327736876 chr11 135006516 16098477 0.11924222235317887 1.691566850976971 chr12 133851895 14842629 0.11088844875898096 0.471820014909625 chr13 115169878 8485894 0.07368154023745688 0.37919674711744555 chr14 107349540 12096898 0.11268700359591667 0.4979683847711674 chr15 102531392 9189728 0.08962843301688521 0.4211948993031926 chr16 90354753 13930153 0.1541717788769784 3.9547002651837473 chr17 81195210 7123379 0.08773151765972402 1.734585299732051 chr18 78077248 10259760 0.1314052462504826 2.856694800162503 chr19 59128983 5428406 0.09180617904420917 1.9687363742241673 chr20 63025520 6469380 0.10264699125052835 0.8008602074516489 chr21 48129895 4736429 0.09840929426503008 1.0529143534050016 chr22 51304566 3089892 0.06022645235903565 0.3520506526731513 chrMT 16571 61677 3.7219841892462737 3.1813432033205733 chrX 155270560 40516371 0.2609404577403469 1.2399623061575595 chrY 59373566 2084353 0.03510574049064191 3.0141541089920074