BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549022.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 = 3,829,481 number of mapped reads = 3,317,644 (86.63%) number of secondary alignments = 0 number of mapped bases = 131,421,018 bp number of sequenced bases = 131,407,258 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,655 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8943 >>>>>>> ACTG content number of A's = 38,347,635 bp (29.18%) number of C's = 27,276,452 bp (20.76%) number of T's = 38,431,044 bp (29.25%) number of G's = 27,350,736 bp (20.81%) number of N's = 1,391 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 338,715 number of insertions = 3,915 mapped reads with insertion percentage = 0.12% number of deletions = 10,536 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.6061X There is a 3.65% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 10424459 0.041823201716315886 0.4622429612381028 chr2 243199373 11068760 0.04551311075954131 0.2843103344554922 chr3 198022430 8867553 0.04478054834495264 0.23912395393379257 chr4 191154276 8524197 0.04459328443168072 0.24225120625673424 chr5 180915260 8076129 0.044640396835512935 0.23962670396153835 chr6 171115067 7596399 0.044393513284251 0.24923559880338245 chr7 159138663 7274566 0.0457121221384146 0.35893818062505 chr8 146364022 6882952 0.04702625622026156 2.4672086948122853 chr9 141213431 5594466 0.03961709562881451 0.2643537515355108 chr10 135534747 6052254 0.04465463015177946 0.2704118209481385 chr11 135006516 5929745 0.04392191707250634 0.3137585343562355 chr12 133851895 5924162 0.04425908202495004 0.24041641106584302 chr13 115169878 4219748 0.036639337240593414 0.2155727165235481 chr14 107349540 3960330 0.03689191402217466 0.2368243777955302 chr15 102531392 3881976 0.03786134104177577 0.21868814741295517 chr16 90354753 3675462 0.04067812569860049 0.23434920207224783 chr17 81195210 3463974 0.042662294980208806 0.24415351086567005 chr18 78077248 3445751 0.044132587767437705 0.3908835661735929 chr19 59128983 2535358 0.04287843070123496 0.40746735478191454 chr20 63025520 2664020 0.04226890948301577 0.23631037390591006 chr21 48129895 1675259 0.03480703625054657 0.22045270566755026 chr22 51304566 1446578 0.028195891960181477 0.2110423501733995 chrMT 16571 15603 0.9415846961559351 1.4262691886724788 chrX 155270560 7844106 0.050518952208325904 0.27440236093348497 chrY 59373566 377211 0.006353180807768899 0.11064903642499224