BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068110.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 = 5,002,116 number of mapped reads = 4,738,526 (94.73%) number of supplementary alignments = 31,191 (0.62%) number of secondary alignments = 0 number of mapped bases = 305,418,412 bp number of sequenced bases = 305,303,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 689,685 duplication rate = 11.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1303 >>>>>>> ACTG content number of A's = 81,163,430 bp (26.58%) number of C's = 54,342,361 bp (17.8%) number of T's = 100,163,858 bp (32.81%) number of G's = 69,599,266 bp (22.8%) number of N's = 34,982 bp (0.01%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,655,346 number of insertions = 19,859 mapped reads with insertion percentage = 0.42% number of deletions = 66,237 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.0987X std coverageData = 0.9887X There is a 6.7% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 31375801 0.12588053291149073 2.209139412143505 chr2 243199373 28226464 0.11606306238297744 1.4973907290589359 chr3 198022430 16323251 0.08243132356268934 0.3967182039959097 chr4 191154276 20543418 0.10747035551535347 0.4998495712806389 chr5 180915260 15000411 0.08291401731396235 0.4058438360023179 chr6 171115067 20877168 0.12200660272657346 0.6570146703565177 chr7 159138663 24133918 0.15165339173422615 0.9734967484790484 chr8 146364022 10774602 0.07361509920791873 1.28473621594013 chr9 141213431 9824216 0.06956998304219376 0.7207689193054948 chr10 135534747 15602492 0.11511802209657719 0.6769165879282211 chr11 135006516 15032841 0.11134900333255025 0.653884214030228 chr12 133851895 12607091 0.09418686974883696 0.4706673865868132 chr13 115169878 7393778 0.06419888714304273 0.4038230277885693 chr14 107349540 6874820 0.06404144815152445 0.41517691367186993 chr15 102531392 8560345 0.08348999104586427 0.4444469334508851 chr16 90354753 6238478 0.06904427042150178 0.4152146155626916 chr17 81195210 9435368 0.11620596830773638 0.5217385795214814 chr18 78077248 7835197 0.10035185922536614 1.3613976595467263 chr19 59128983 5695540 0.09632399731955478 1.3504246627331273 chr20 63025520 4200202 0.0666428773614244 0.40043586470915044 chr21 48129895 5140769 0.10681030989159648 0.4786876345915363 chr22 51304566 2975227 0.057991466100697546 0.32200057387326314 chrMT 16571 500003 30.173375173495867 18.709654786782945 chrX 155270560 19391385 0.1248877121329375 0.6049214552050383 chrY 59373566 855627 0.01441090804618338 0.4603436129046162