BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819021.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 = 2,069,551 number of mapped reads = 1,996,315 (96.46%) number of supplementary alignments = 32,451 (1.57%) number of secondary alignments = 0 number of mapped bases = 184,697,299 bp number of sequenced bases = 184,580,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 942,137 duplication rate = 37.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9678 >>>>>>> ACTG content number of A's = 54,004,670 bp (29.26%) number of C's = 36,872,355 bp (19.98%) number of T's = 53,044,277 bp (28.74%) number of G's = 40,650,083 bp (22.02%) number of N's = 9,039 bp (0%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,218,602 number of insertions = 33,321 mapped reads with insertion percentage = 1.63% number of deletions = 61,742 mapped reads with deletion percentage = 3.03% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0597X std coverageData = 0.7671X There is a 2.64% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% 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 18908415 0.07586105472531601 1.3468530750092016 chr2 243199373 14398364 0.05920395197729395 1.148098144285133 chr3 198022430 10956642 0.05533030778382025 0.45327471743694103 chr4 191154276 10214938 0.053438187278635606 0.5380968692053967 chr5 180915260 9878288 0.05460174006327603 0.4672866155770341 chr6 171115067 7907456 0.04621133684271064 0.4941871861102773 chr7 159138663 8607652 0.05408900538519668 0.8303880073606126 chr8 146364022 16852793 0.11514300283439874 0.7289708597670961 chr9 141213431 7936178 0.05619988087393755 0.6708957107493483 chr10 135534747 9712137 0.07165791219575597 0.9443671575725059 chr11 135006516 6037581 0.044720663704854065 0.50659791405565 chr12 133851895 8686274 0.06489466585437584 0.5116089672092964 chr13 115169878 3917728 0.034016950161221846 0.3558208909107586 chr14 107349540 4429702 0.041264284877233756 0.4257449936770192 chr15 102531392 4696252 0.04580306487987601 0.4165618407729472 chr16 90354753 5919317 0.06551196039460148 0.9384272511623998 chr17 81195210 6514148 0.08022823021210242 0.6275540511680268 chr18 78077248 4331345 0.05547512381583941 0.7812295815019326 chr19 59128983 3765623 0.0636848937516818 1.182913113752304 chr20 63025520 5187030 0.08230047130114912 0.600900641425796 chr21 48129895 2763935 0.05742657448141119 0.5318345130204433 chr22 51304566 1514360 0.029517060918125688 0.37006767166684384 chrMT 16571 24836 1.4987628990404924 2.7124443305593786 chrX 155270560 10850808 0.0698832283467001 0.5774919657243954 chrY 59373566 685497 0.011545491473427753 0.8213303528044462