BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124944.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,531,598 number of mapped reads = 4,396,442 (97.02%) number of supplementary alignments = 5,879 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,225,418 number of mapped paired reads (second in pair) = 2,171,024 number of mapped paired reads (both in pair) = 4,326,886 number of mapped paired reads (singletons) = 69,556 number of mapped bases = 273,308,343 bp number of sequenced bases = 273,187,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,197 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 31,147.2884 std insert size = 1,656,087.3759 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 51.9093 >>>>>>> ACTG content number of A's = 74,283,002 bp (27.19%) number of C's = 49,578,066 bp (18.15%) number of T's = 80,296,761 bp (29.39%) number of G's = 69,027,223 bp (25.27%) number of N's = 2,339 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,780,734 number of insertions = 29,704 mapped reads with insertion percentage = 0.67% number of deletions = 78,763 mapped reads with deletion percentage = 1.77% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0883X std coverageData = 0.6375X There is a 7.08% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 17169128 0.06888298986424592 0.6049985074087989 chr2 243199373 26311392 0.1081885683973371 0.9370906809769747 chr3 198022430 17372141 0.08772814776588693 0.3464077551068091 chr4 191154276 15712750 0.08219931214094316 0.4285302730895011 chr5 180915260 21171388 0.11702378229453944 0.42072794708778916 chr6 171115067 13498559 0.07888585871868314 0.47666809016557926 chr7 159138663 17557902 0.11033083770472547 0.9155527323873829 chr8 146364022 18687111 0.12767557726720574 0.46866436049004734 chr9 141213431 7618314 0.05394893351185554 0.49129462547903097 chr10 135534747 17139560 0.12645878919890557 1.400400091918485 chr11 135006516 14099861 0.10443837392263348 0.48043015488971047 chr12 133851895 10092564 0.07540097956775285 0.3267026334161442 chr13 115169878 9444070 0.0820012156303578 0.33633308675120366 chr14 107349540 5735105 0.05342458849846958 0.30621849743602675 chr15 102531392 8610329 0.08397749052309755 0.3466119707238827 chr16 90354753 9141141 0.10116945369769313 1.0436198593041868 chr17 81195210 9579366 0.11797944730976126 0.7250807187203866 chr18 78077248 5653678 0.0724113380635547 0.7610766477002419 chr19 59128983 4234322 0.07161161557607036 0.5407069911399338 chr20 63025520 5515359 0.087509932484492 0.41278391489754157 chr21 48129895 2487275 0.05167837993413449 0.3389828548118317 chr22 51304566 3457719 0.06739593119255702 0.324913176214254 chrMT 16571 50852 3.068734536238006 2.778013143573043 chrX 155270560 12285476 0.07912302241970404 0.3862800544739226 chrY 59373566 682981 0.011503115713144128 0.6696069556289885