BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008713.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 = 1,884,594 number of mapped reads = 1,222,539 (64.87%) number of supplementary alignments = 4,474 (0.24%) number of secondary alignments = 0 number of mapped bases = 76,696,853 bp number of sequenced bases = 76,656,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,288 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6804 >>>>>>> ACTG content number of A's = 21,557,140 bp (28.12%) number of C's = 12,873,971 bp (16.79%) number of T's = 23,524,076 bp (30.69%) number of G's = 18,699,125 bp (24.39%) number of N's = 1,893 bp (0%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 808,541 number of insertions = 6,078 mapped reads with insertion percentage = 0.49% number of deletions = 25,892 mapped reads with deletion percentage = 2.09% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2112X There is a 2.16% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% 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 5521904 0.02215402303852234 0.24885541350608578 chr2 243199373 6840822 0.028128452452877005 0.2647291985613727 chr3 198022430 5375991 0.02714839425008571 0.18548542877934593 chr4 191154276 3195551 0.016717130617575095 0.1477438949849319 chr5 180915260 3302959 0.018256939740738286 0.1506550589001314 chr6 171115067 4635543 0.0270902094203078 0.19432626707188458 chr7 159138663 5746305 0.03610879274510431 0.3224293529224869 chr8 146364022 9939062 0.06790645586385977 0.3414505590126105 chr9 141213431 1946631 0.01378502728964924 0.16493889829399164 chr10 135534747 3014996 0.022245188534568187 0.18382518734914283 chr11 135006516 2769587 0.020514469094217645 0.18692699297814058 chr12 133851895 2992515 0.022356911719479206 0.16791171270797203 chr13 115169878 1687277 0.014650332441960215 0.1348937283360739 chr14 107349540 2202635 0.02051834595658258 0.16203112761668298 chr15 102531392 3064806 0.029891391701772664 0.19837478152426313 chr16 90354753 1824081 0.020187991659940677 0.1639335912915706 chr17 81195210 1643108 0.020236513951992982 0.17027943344698368 chr18 78077248 1095842 0.014035356369117928 0.2658866297458559 chr19 59128983 1164269 0.019690326823310997 0.18128721953406074 chr20 63025520 2271374 0.036038956917769184 0.2143445007276899 chr21 48129895 667918 0.013877404054174645 0.1348706533581469 chr22 51304566 820515 0.015993020972051495 0.14001578288808145 chrMT 16571 62188 3.75282119365156 3.3644264943627027 chrX 155270560 4706230 0.030309866854347663 0.20159064606892768 chrY 59373566 204744 0.003448403284384165 0.07818107375257637