BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549118.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 = 10,669,153 number of mapped reads = 6,136,093 (57.51%) number of secondary alignments = 0 number of mapped bases = 243,636,833 bp number of sequenced bases = 243,614,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 212,790 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6824 >>>>>>> ACTG content number of A's = 72,510,497 bp (29.76%) number of C's = 48,667,112 bp (19.98%) number of T's = 73,342,014 bp (30.11%) number of G's = 49,084,750 bp (20.15%) number of N's = 10,147 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 723,848 number of insertions = 6,020 mapped reads with insertion percentage = 0.1% number of deletions = 17,966 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0787X std coverageData = 0.4662X There is a 6.32% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% 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% 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 19076529 0.07653553248318687 0.7726137814311326 chr2 243199373 21925541 0.09015459509428916 0.4523911212704317 chr3 198022430 17600461 0.08888114846383816 0.3585530494144147 chr4 191154276 17526196 0.09168613104945662 0.3721945719760805 chr5 180915260 15942391 0.08812076438438637 0.3578419220269148 chr6 171115067 14684008 0.08581364725760823 0.38370602262580766 chr7 159138663 13716266 0.08619065751482403 0.6856355061839149 chr8 146364022 12978050 0.08866967320698525 0.5578049904944509 chr9 141213431 10395717 0.0736170555901301 0.42623295883366447 chr10 135534747 11141643 0.08220506731015627 0.4388009619239232 chr11 135006516 11470907 0.0849655804761305 0.41605535606945715 chr12 133851895 11118926 0.08306887250270159 0.35377807497770414 chr13 115169878 8464485 0.0734956496176891 0.3246294331489341 chr14 107349540 7790222 0.07256875064392451 0.37044209815061324 chr15 102531392 6926754 0.06755739744565255 0.31119309885805824 chr16 90354753 6269272 0.06938508259770242 0.3395949663387881 chr17 81195210 5381361 0.0662768283991137 0.3232122519937709 chr18 78077248 6867866 0.08796244970109603 0.7794375191399496 chr19 59128983 3564929 0.06029072071136417 0.6096566749235728 chr20 63025520 4570232 0.07251399115786748 0.33457122427421637 chr21 48129895 3230956 0.06712991998008722 0.34120673595038653 chr22 51304566 2233079 0.043525931005828994 0.2528270114052605 chrMT 16571 41326 2.493874841590731 3.3108255185638784 chrX 155270560 8758925 0.05641072589678301 0.3201423041264535 chrY 59373566 1960791 0.033024646018398156 0.26180565378455634