BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549122.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,301,924 number of mapped reads = 7,237,786 (58.83%) number of secondary alignments = 0 number of mapped bases = 287,350,675 bp number of sequenced bases = 287,321,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 303,067 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0545 >>>>>>> ACTG content number of A's = 84,198,561 bp (29.3%) number of C's = 59,248,358 bp (20.62%) number of T's = 84,694,008 bp (29.48%) number of G's = 59,168,184 bp (20.59%) number of N's = 12,086 bp (0%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 892,912 number of insertions = 7,145 mapped reads with insertion percentage = 0.1% number of deletions = 23,124 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.0928X std coverageData = 0.6724X There is a 7.2% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.33% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23390169 0.09384196880295836 1.2149111739268854 chr2 243199373 24779998 0.10189170183428063 0.5621014908706052 chr3 198022430 19501181 0.0984796570772311 0.38503365506633935 chr4 191154276 18950880 0.09913918954133152 0.4559012198694199 chr5 180915260 17883726 0.09885139595189482 0.3964187716816673 chr6 171115067 16849215 0.09846716186599745 0.40795144079498713 chr7 159138663 16051149 0.10086266088587159 0.8068289635443127 chr8 146364022 15029262 0.10268412820740878 1.4427694387662198 chr9 141213431 12254863 0.08678255965609957 0.5063936556197665 chr10 135534747 13699644 0.1010784636651146 0.6259137469467178 chr11 135006516 13369036 0.09902511668399769 0.5206282989447248 chr12 133851895 13073823 0.09767379834256362 0.4008970747666516 chr13 115169878 10594356 0.09198894870757786 0.3716361629664646 chr14 107349540 8969636 0.08355542091749997 0.4388850352240094 chr15 102531392 8504914 0.08294936637551942 0.3494415544279919 chr16 90354753 8073598 0.08935443606381172 0.41332560719368855 chr17 81195210 7555242 0.09305034127013158 0.40518496920910185 chr18 78077248 7676567 0.0983201533947508 0.984239575673315 chr19 59128983 5447884 0.09213559448502606 0.9526785297297403 chr20 63025520 6120846 0.09711694564360596 0.4136073529481088 chr21 48129895 3804054 0.07903723870579814 0.4379225007213428 chr22 51304566 3284073 0.06401132016203002 0.32127780512483295 chrMT 16571 128593 7.760123106632068 9.728640488351507 chrX 155270560 9652915 0.06216835309926106 0.37268345809892356 chrY 59373566 2705051 0.04555985402662188 0.522825531233662