BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238323.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,777,068 number of mapped reads = 1,335,833 (75.17%) number of supplementary alignments = 19,037 (1.07%) number of secondary alignments = 0 number of mapped bases = 86,335,927 bp number of sequenced bases = 86,295,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,379 duplication rate = 8.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1771 >>>>>>> ACTG content number of A's = 23,802,453 bp (27.58%) number of C's = 16,285,875 bp (18.87%) number of T's = 26,976,424 bp (31.26%) number of G's = 19,210,271 bp (22.26%) number of N's = 20,962 bp (0.02%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 736,326 number of insertions = 6,351 mapped reads with insertion percentage = 0.47% number of deletions = 23,516 mapped reads with deletion percentage = 1.74% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.3143X There is a 1.74% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 6667908 0.02675182101151114 0.45009718432492796 chr2 243199373 7694932 0.03164042696771262 0.3694886167461011 chr3 198022430 5788036 0.029229193884753358 0.25803385160290665 chr4 191154276 5453028 0.02852684289416576 0.2582926130806364 chr5 180915260 5570547 0.030790918355919784 0.265842090867418 chr6 171115067 5284018 0.030879910767881123 0.29537991243569 chr7 159138663 4664461 0.029310671034103133 0.3578889707855425 chr8 146364022 4401399 0.03007159095423054 0.3944286234244927 chr9 141213431 3552314 0.025155638347176764 0.28468462234015335 chr10 135534747 3960249 0.02921943699057482 0.2989237946149695 chr11 135006516 3894709 0.02884830388482879 0.2991555341711954 chr12 133851895 3889644 0.02905931215990629 0.25925400643421476 chr13 115169878 2581278 0.02241278748250476 0.226794101979165 chr14 107349540 2505663 0.023341161964923186 0.24040316503285938 chr15 102531392 2651717 0.025862489021898777 0.24750176419736677 chr16 90354753 2602046 0.028798108717092062 0.26486093336342476 chr17 81195210 2229208 0.027454920062402695 0.25990635254476285 chr18 78077248 2211197 0.028320631895222537 0.4171050032926628 chr19 59128983 1748402 0.029569289226571004 0.3597015846312235 chr20 63025520 1721081 0.0273076842523473 0.2576119631637033 chr21 48129895 1171263 0.024335457203885445 0.23758345391639052 chr22 51304566 843069 0.01643263096699814 0.1874244522288975 chrMT 16571 311741 18.812443425260998 13.07307242003134 chrX 155270560 4688129 0.03019328970024968 0.2684404226003514 chrY 59373566 249888 0.0042087416477561744 0.10427529027022474