BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,296,973 number of mapped reads = 1,784,201 (77.68%) number of supplementary alignments = 6,992 (0.3%) number of secondary alignments = 0 number of mapped bases = 108,567,638 bp number of sequenced bases = 108,492,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,227 duplication rate = 5.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5912 >>>>>>> ACTG content number of A's = 29,303,664 bp (27.01%) number of C's = 19,466,117 bp (17.94%) number of T's = 33,551,889 bp (30.93%) number of G's = 26,081,497 bp (24.04%) number of N's = 89,321 bp (0.08%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,125,601 number of insertions = 10,483 mapped reads with insertion percentage = 0.58% number of deletions = 46,932 mapped reads with deletion percentage = 2.59% homopolymer indels = 48.21% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.3457X There is a 2.61% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 9557638 0.03834549322948327 0.4197403486844262 chr2 243199373 9006552 0.03703361521413133 0.45763180000296844 chr3 198022430 7591342 0.03833576832685065 0.2897414477910596 chr4 191154276 6547852 0.03425427951190587 0.27459625670877114 chr5 180915260 5899691 0.032610245260681715 0.25551019217608145 chr6 171115067 5977349 0.034931751509643505 0.29735782225031354 chr7 159138663 6125420 0.038491086229623536 0.4923578099453904 chr8 146364022 5541725 0.03786261763153789 0.355703023105871 chr9 141213431 4742120 0.03358122500401538 0.3407886096184614 chr10 135534747 5516966 0.04070517798657196 0.3602548614094208 chr11 135006516 4506891 0.03338276650291457 0.36444380136167515 chr12 133851895 5641409 0.04214665022112687 0.3097906021878867 chr13 115169878 3552403 0.03084489678802994 0.2653443875350302 chr14 107349540 3146656 0.029312244840546127 0.28550661917993564 chr15 102531392 3156660 0.03078725391731734 0.26333836398899957 chr16 90354753 3621620 0.0400822300958534 0.3192537662390168 chr17 81195210 2562590 0.0315608519271026 0.2656595592761129 chr18 78077248 2694941 0.0345163420718927 0.5411196434955701 chr19 59128983 2040177 0.03450384052774931 0.34646515407742234 chr20 63025520 2144286 0.03402250390000749 0.2781774316852488 chr21 48129895 1362240 0.028303406853474333 0.2590511148010198 chr22 51304566 1070694 0.020869370574151235 0.2043325021968717 chrMT 16571 60109 3.6273610524410116 4.290889831771197 chrX 155270560 6125977 0.03945356415279239 0.3033141800557428 chrY 59373566 374330 0.006304657530591981 0.15052190581885433