BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514752.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 5,948,776 number of mapped reads = 3,732,946 (62.75%) number of supplementary alignments = 504,936 (8.49%) number of secondary alignments = 0 number of mapped bases = 358,858,725 bp number of sequenced bases = 358,736,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 902,140 duplication rate = 18.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6997 >>>>>>> ACTG content number of A's = 112,866,662 bp (31.46%) number of C's = 66,525,430 bp (18.54%) number of T's = 110,544,832 bp (30.82%) number of G's = 68,774,293 bp (19.17%) number of N's = 25,111 bp (0.01%) GC percentage = 37.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,660,191 number of insertions = 125,181 mapped reads with insertion percentage = 3.28% number of deletions = 56,189 mapped reads with deletion percentage = 1.47% homopolymer indels = 60.9% >>>>>>> Coverage mean coverageData = 0.1159X std coverageData = 1.639X There is a 2.67% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% 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 23785425 0.09542774619606664 1.3240725337029264 chr2 243199373 27008943 0.11105679536435319 1.3165577846220158 chr3 198022430 30426351 0.15365103337031064 1.6697330725548927 chr4 191154276 30681461 0.16050627609292925 1.7662806264407926 chr5 180915260 20654086 0.11416442150872182 1.5243225517514913 chr6 171115067 23101813 0.13500747423954199 1.4994528436073649 chr7 159138663 15959103 0.1002842596459416 1.3586615049228832 chr8 146364022 18149848 0.12400484594499596 1.4489510970732031 chr9 141213431 19581164 0.13866360912936107 1.4821352271216075 chr10 135534747 18582787 0.13710718034542094 1.6405262848602924 chr11 135006516 17273834 0.127948150295205 1.3075866959071292 chr12 133851895 22258029 0.16628848624070658 1.7300244244058312 chr13 115169878 12828117 0.11138430658058003 1.2554029114075778 chr14 107349540 9687023 0.09023814168183673 1.2496465021247045 chr15 102531392 5080916 0.049554735392649304 0.8143412113308897 chr16 90354753 6488720 0.07181382035320268 1.104160187345956 chr17 81195210 8055443 0.09921081551485611 1.0905109809804612 chr18 78077248 8619707 0.11039972874043921 1.4012761637863465 chr19 59128983 3157466 0.05339963313761037 1.0332246134984313 chr20 63025520 8163341 0.12952437361881347 1.3960922626418717 chr21 48129895 4743700 0.09856036461330323 1.1785008838161404 chr22 51304566 3123595 0.06088337244681107 0.8626837543396126 chrMT 16571 4733543 285.6522237644077 176.60176510948702 chrX 155270560 12132184 0.07813576507999971 1.928194431163541 chrY 59373566 4582126 0.07717451230737934 1.1663114976379292