BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524363.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,118,833 number of mapped reads = 1,032,193 (92.26%) number of supplementary alignments = 5,174 (0.46%) number of secondary alignments = 0 number of mapped bases = 61,603,896 bp number of sequenced bases = 61,586,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,645 duplication rate = 3.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7002 >>>>>>> ACTG content number of A's = 16,301,224 bp (26.47%) number of C's = 12,114,718 bp (19.67%) number of T's = 18,170,452 bp (29.5%) number of G's = 14,991,017 bp (24.34%) number of N's = 9,045 bp (0.01%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 311,595 number of insertions = 5,287 mapped reads with insertion percentage = 0.51% number of deletions = 10,847 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.198X There is a 1.75% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 4986479 0.02000588395725602 0.2661610883424099 chr2 243199373 5186843 0.021327534425839165 0.2528318059541933 chr3 198022430 3959038 0.019992876564538672 0.1560530873101993 chr4 191154276 3856274 0.02017362143654061 0.18060833239550664 chr5 180915260 3696416 0.0204317535181941 0.158786208589751 chr6 171115067 3445192 0.020133773491728815 0.16180655757388926 chr7 159138663 3395082 0.021334111623144653 0.2562893473239434 chr8 146364022 2912434 0.019898564962911446 0.2056696154998073 chr9 141213431 2523421 0.017869553782033663 0.17234465263522905 chr10 135534747 3037212 0.022409102220849682 0.21675725994036552 chr11 135006516 2872927 0.021279913630242855 0.18890356975764858 chr12 133851895 2828550 0.021131938401021517 0.16326177019665586 chr13 115169878 1869058 0.016228705217522243 0.1415090260412737 chr14 107349540 1870643 0.017425719756228114 0.15018207911987072 chr15 102531392 1851935 0.018062126767965855 0.14875343538526034 chr16 90354753 1891737 0.02093677351981694 0.17142299736729452 chr17 81195210 1758387 0.021656289823008032 0.1722748990052338 chr18 78077248 1639964 0.02100437761330932 0.3051990472585966 chr19 59128983 1338584 0.02263837346906508 0.22535741817443913 chr20 63025520 1395464 0.022141253257410648 0.1717258555607163 chr21 48129895 840494 0.017463034149565463 0.16967833751047917 chr22 51304566 844274 0.016456118155253472 0.14596994477772315 chrMT 16571 5787 0.34922454891074767 0.6464059541041276 chrX 155270560 3364000 0.021665407788830027 0.1707499864790429 chrY 59373566 233701 0.0039361119054226925 0.14234178136944572