BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549146.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 = 13,200,525 number of mapped reads = 11,555,007 (87.53%) number of secondary alignments = 0 number of mapped bases = 458,571,525 bp number of sequenced bases = 458,527,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 712,744 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3951 >>>>>>> ACTG content number of A's = 129,144,912 bp (28.17%) number of C's = 98,808,013 bp (21.55%) number of T's = 131,236,499 bp (28.62%) number of G's = 99,246,136 bp (21.64%) number of N's = 92,390 bp (0.02%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,424,764 number of insertions = 12,152 mapped reads with insertion percentage = 0.11% number of deletions = 34,832 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.1481X std coverageData = 0.8273X There is a 9.83% of reference with a coverageData >= 1X There is a 3.03% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 38009931 0.15249683570497505 1.3291685712949508 chr2 243199373 38957369 0.16018696314648806 0.8659657828196431 chr3 198022430 31109035 0.15709854181670227 0.5597063560992175 chr4 191154276 28391255 0.14852534609270263 0.5545189136554355 chr5 180915260 28061844 0.1551104312593642 0.5711601760034194 chr6 171115067 26390613 0.15422728964013438 0.6327627301113296 chr7 159138663 25598545 0.16085685601116304 1.2732431709738965 chr8 146364022 23503678 0.1605837123005543 0.8361462703418592 chr9 141213431 19880456 0.14078303925637214 0.8331568042924149 chr10 135534747 22208427 0.1638578113109253 0.7563350870574781 chr11 135006516 21155761 0.15670177726829126 0.7554461043347201 chr12 133851895 21215530 0.15850003468385712 0.5923989926024313 chr13 115169878 14043928 0.12194098182512618 0.48263597761664484 chr14 107349540 14550462 0.1355428444313781 0.6905118416000285 chr15 102531392 14076474 0.13728940693597527 0.5234455694714428 chr16 90354753 14223459 0.15741793904300752 0.6305867745844804 chr17 81195210 13840115 0.1704548211649431 0.6501062802503081 chr18 78077248 12027228 0.15404267322536777 1.6258477583197768 chr19 59128983 10233827 0.173076323670238 1.2378645975351554 chr20 63025520 10501487 0.16662277439361073 0.6245930176459047 chr21 48129895 5893903 0.12245825593427952 0.5808769433173209 chr22 51304566 6268908 0.12219006004260907 0.5384568996983234 chrMT 16571 91470 5.519884134934524 8.483492380922431 chrX 155270560 15099938 0.09724920165162024 0.5538556913526428 chrY 59373566 3237882 0.054534066557498 0.3702954397572883