BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082980.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 = 2,626,410 number of mapped reads = 2,013,991 (76.68%) number of supplementary alignments = 13,718 (0.52%) number of secondary alignments = 0 number of mapped bases = 135,582,532 bp number of sequenced bases = 135,525,848 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,566 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2681 >>>>>>> ACTG content number of A's = 38,481,925 bp (28.39%) number of C's = 24,944,629 bp (18.41%) number of T's = 42,747,034 bp (31.54%) number of G's = 29,339,098 bp (21.65%) number of N's = 13,162 bp (0.01%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,337,142 number of insertions = 12,410 mapped reads with insertion percentage = 0.61% number of deletions = 33,171 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.4166X There is a 3.84% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 12374445 0.049646596467256145 0.7898363791204475 chr2 243199373 12844412 0.05281433024089252 0.5167571336890975 chr3 198022430 11150934 0.05631146936233436 0.26268216797024346 chr4 191154276 7152948 0.03741976454662202 0.2160655962288519 chr5 180915260 8999604 0.04974485844919881 0.24912536748434058 chr6 171115067 8902248 0.05202492191993824 0.3384183369554815 chr7 159138663 7623363 0.04790390252304683 0.48416182641197336 chr8 146364022 11151653 0.07619121726512817 0.4953380402723215 chr9 141213431 3831438 0.02713224919802423 0.39791424205799836 chr10 135534747 4513804 0.03330366640224001 0.2962109931661045 chr11 135006516 5976991 0.04427187055178877 0.36534996389670493 chr12 133851895 4654669 0.03477477102584166 0.21238819458387123 chr13 115169878 3223028 0.027984991006068445 0.1816259668063982 chr14 107349540 3003387 0.027977642009458074 0.23243534048791423 chr15 102531392 2832554 0.027626212272627685 0.1811265866458878 chr16 90354753 4415997 0.04887398673980106 0.3049434411816335 chr17 81195210 3448487 0.04247155712756947 0.29411667655467844 chr18 78077248 3794972 0.048605350434482525 0.9221369732432431 chr19 59128983 2287072 0.03867937319334581 0.5138439137620934 chr20 63025520 3182910 0.050501923665207366 0.25948734603338536 chr21 48129895 1891806 0.03930625653764672 0.22847870529957592 chr22 51304566 1931373 0.0376452458442003 0.21333372483024102 chrMT 16571 5753 0.3471727717096132 0.6472020867024532 chrX 155270560 6134781 0.03951026517840858 0.2714911937205489 chrY 59373566 253903 0.0042763643335823895 0.09312125321840592