BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080821.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,970,769 number of mapped reads = 2,769,694 (93.23%) number of supplementary alignments = 18,748 (0.63%) number of secondary alignments = 0 number of mapped bases = 193,016,302 bp number of sequenced bases = 192,942,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,328 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1275 >>>>>>> ACTG content number of A's = 55,959,979 bp (29%) number of C's = 36,366,497 bp (18.85%) number of T's = 60,478,034 bp (31.35%) number of G's = 40,111,026 bp (20.79%) number of N's = 27,153 bp (0.01%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,572,511 number of insertions = 14,651 mapped reads with insertion percentage = 0.52% number of deletions = 41,432 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0623X std coverageData = 0.492X There is a 4.59% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% 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% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 24527784 0.0984061098888897 0.943984287561491 chr2 243199373 14681921 0.06036989659508703 0.441774997353473 chr3 198022430 11693792 0.059052865879890476 0.32424970258323227 chr4 191154276 11411227 0.05969642551966768 0.33326425265324194 chr5 180915260 15029201 0.08307315259088703 0.36795547063670886 chr6 171115067 13716493 0.08015946953402998 0.45524086367223665 chr7 159138663 13986646 0.08788967895249943 0.7276630001539147 chr8 146364022 8561666 0.05849570053493064 0.7325572968272515 chr9 141213431 6495422 0.045997196966342385 0.33312411098344447 chr10 135534747 7884223 0.05817123043731361 0.5765468398058458 chr11 135006516 7418154 0.05494663679788611 0.3295990641479822 chr12 133851895 7455773 0.05570166190026671 0.3024440811458738 chr13 115169878 8250544 0.07163803716107088 0.3429807139550468 chr14 107349540 4956425 0.04617090115150936 0.28340932236213034 chr15 102531392 4468704 0.04358376408271137 0.264742528051248 chr16 90354753 4243095 0.04696039620627373 0.3153610158163055 chr17 81195210 4687102 0.05772633631959324 0.3219154242004112 chr18 78077248 2517743 0.032246820482197326 0.536351904229923 chr19 59128983 2676469 0.04526492532435405 0.6207025261824721 chr20 63025520 3320703 0.05268822851441765 0.2984332898331574 chr21 48129895 3003240 0.062398640179871574 0.3459470733402191 chr22 51304566 1584166 0.03087768055576184 0.2209237160900615 chrMT 16571 67460 4.0709673526039465 2.863606704598043 chrX 155270560 9898580 0.0637505268223416 0.3377263677731313 chrY 59373566 479769 0.008080515157199755 0.20065830913540694