BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818884.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 = 1,487,441 number of mapped reads = 1,457,978 (98.02%) number of supplementary alignments = 21,259 (1.43%) number of secondary alignments = 0 number of mapped bases = 135,118,931 bp number of sequenced bases = 135,033,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 238,591 duplication rate = 13.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3748 >>>>>>> ACTG content number of A's = 38,319,481 bp (28.38%) number of C's = 27,694,134 bp (20.51%) number of T's = 39,296,240 bp (29.1%) number of G's = 29,721,392 bp (22.01%) number of N's = 1,954 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 839,729 number of insertions = 21,357 mapped reads with insertion percentage = 1.42% number of deletions = 43,354 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.06% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.5341X There is a 3.31% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 13350053 0.05356076123878544 0.8073043406919607 chr2 243199373 10115369 0.04159290739618807 0.7382641417277094 chr3 198022430 8327648 0.042054064279485916 0.25717277430552155 chr4 191154276 6483615 0.03391823157542131 0.3114411561421577 chr5 180915260 5925948 0.03275537950751087 0.23919406745028352 chr6 171115067 6638308 0.03879440961210038 0.2735542537799682 chr7 159138663 11768744 0.07395276407468623 1.164555100099969 chr8 146364022 11284520 0.07709900182983494 0.43026220862734454 chr9 141213431 4958550 0.03511386958652679 0.4325004069864777 chr10 135534747 6449978 0.0475891101194884 0.7621881855754631 chr11 135006516 6014307 0.044548272025625786 0.32312801624796356 chr12 133851895 5276884 0.03942330439176823 0.2512655337192206 chr13 115169878 3967318 0.03444753149777583 0.22795675798957515 chr14 107349540 4022193 0.03746819036206397 0.2602741306627592 chr15 102531392 3790925 0.03697331057399474 0.23811448791185255 chr16 90354753 3552232 0.03931427934953239 0.5276002199181853 chr17 81195210 3710956 0.04570412466449683 0.3394458557614863 chr18 78077248 2464096 0.03155971890812545 0.4859648034730408 chr19 59128983 2560565 0.043304736020912116 0.7196812325808689 chr20 63025520 5834426 0.09257243732380153 0.40731429988097584 chr21 48129895 1335892 0.027755971626366522 0.25511159019469565 chr22 51304566 1397482 0.02723894009745643 0.22453343365442102 chrMT 16571 292347 17.642085571178566 10.858918249132168 chrX 155270560 5117033 0.032955590551099964 0.27475053492639756 chrY 59373566 479542 0.008076691906967488 0.6405383720686966