BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004152.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 = 1,623,082 number of mapped reads = 1,401,393 (86.34%) number of supplementary alignments = 10,594 (0.65%) number of secondary alignments = 0 number of mapped bases = 92,328,912 bp number of sequenced bases = 92,284,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,030 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5344 >>>>>>> ACTG content number of A's = 26,029,512 bp (28.21%) number of C's = 17,075,052 bp (18.5%) number of T's = 28,130,251 bp (30.48%) number of G's = 20,987,830 bp (22.74%) number of N's = 61,614 bp (0.07%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 872,298 number of insertions = 7,563 mapped reads with insertion percentage = 0.54% number of deletions = 26,132 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.3127X There is a 2.68% of reference with a coverageData >= 1X There is a 0.2% 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 7725968 0.030996785360065362 0.5690468049719509 chr2 243199373 7457316 0.03066338497509202 0.3510824821341631 chr3 198022430 6233013 0.031476297912312254 0.19276965087275802 chr4 191154276 5810259 0.030395652776294683 0.19732920857998468 chr5 180915260 4743485 0.026219374750366554 0.17604243858366858 chr6 171115067 5354488 0.031291738909233514 0.21104687861098764 chr7 159138663 6473096 0.04067582244297226 0.45656146418330046 chr8 146364022 6822705 0.04661463183896381 0.36099412955288035 chr9 141213431 3750509 0.026559152153168772 0.30984254988553395 chr10 135534747 4264702 0.031465746566081684 0.3411261177920187 chr11 135006516 4396481 0.0325649541241402 0.2777289016625074 chr12 133851895 4005066 0.029921623448065492 0.19254523627990727 chr13 115169878 2778706 0.024127020434978667 0.16595071108034098 chr14 107349540 2196190 0.02045830843802405 0.18978028789057422 chr15 102531392 2445580 0.0238520120745069 0.17251440827155848 chr16 90354753 2466896 0.027302337930136335 0.22784178569800284 chr17 81195210 2085808 0.02568880602685799 0.18609628519643878 chr18 78077248 2371428 0.03037284305922258 0.5868363108412745 chr19 59128983 1617610 0.027357311388223945 0.38438704723020867 chr20 63025520 1681330 0.02667697148710554 0.19014632514726323 chr21 48129895 984573 0.02045657901393718 0.17666884061033478 chr22 51304566 959716 0.01870624926444169 0.14580840704866935 chrMT 16571 16380 0.9884738398406855 1.2958976757621907 chrX 155270560 5440422 0.03503833566388889 0.22864841256083648 chrY 59373566 247185 0.004163216337721739 0.10104647228034029