BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818963.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,952,718 number of mapped reads = 2,886,828 (97.77%) number of supplementary alignments = 44,539 (1.51%) number of secondary alignments = 0 number of mapped bases = 267,459,314 bp number of sequenced bases = 267,303,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,498,951 duplication rate = 41.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3564 >>>>>>> ACTG content number of A's = 78,550,007 bp (29.39%) number of C's = 55,844,830 bp (20.89%) number of T's = 76,779,813 bp (28.72%) number of G's = 56,115,137 bp (20.99%) number of N's = 13,460 bp (0.01%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,666,477 number of insertions = 40,751 mapped reads with insertion percentage = 1.38% number of deletions = 84,617 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0864X std coverageData = 0.9388X There is a 3.43% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% 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% 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 26188390 0.10506850452340498 1.5618693840095934 chr2 243199373 21847908 0.08983537963315391 1.2763074552726175 chr3 198022430 14749297 0.07448296134937846 0.5695235299619464 chr4 191154276 14639124 0.07658277024365387 0.6659569037916346 chr5 180915260 14584552 0.08061537760827915 0.6120421609672011 chr6 171115067 11273822 0.0658844495558068 0.6477479557469571 chr7 159138663 13030822 0.0818834452567947 1.1622949822169413 chr8 146364022 23753179 0.16228837302653518 0.9512253654293217 chr9 141213431 11700621 0.08285770636080643 0.9071679592161433 chr10 135534747 14173570 0.10457517584033266 1.1546732640303123 chr11 135006516 9090953 0.06733714245318352 0.6496139289422657 chr12 133851895 12306063 0.09193790644503015 0.6456890714631252 chr13 115169878 5577558 0.04842896508060901 0.4553678850698164 chr14 107349540 6459311 0.06017083072736036 0.5515735941950719 chr15 102531392 7063734 0.068893378527427 0.5516832603194571 chr16 90354753 8446136 0.09347749531228312 0.9969520491001452 chr17 81195210 9747398 0.12004892899470301 0.846093294723225 chr18 78077248 6190804 0.07929075573975149 1.0880267370416057 chr19 59128983 5353270 0.09053546549244725 1.4963169190549401 chr20 63025520 7690067 0.12201512974426867 0.8005226602396907 chr21 48129895 3575163 0.07428154580432805 0.6190293152700023 chr22 51304566 2124115 0.04140206546138603 0.4598174278114957 chrMT 16571 37637 2.2712570152676363 3.0166451313452787 chrX 155270560 16919992 0.10897102451359743 0.776379815360817 chrY 59373566 935828 0.015761694354016063 0.9410735810563664