BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237269.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 = 3,365,065 number of mapped reads = 3,118,905 (92.68%) number of supplementary alignments = 23,033 (0.68%) number of secondary alignments = 0 number of mapped bases = 223,690,559 bp number of sequenced bases = 223,568,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,242 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9649 >>>>>>> ACTG content number of A's = 67,820,976 bp (30.34%) number of C's = 42,290,969 bp (18.92%) number of T's = 69,597,893 bp (31.13%) number of G's = 43,854,986 bp (19.62%) number of N's = 4,006 bp (0%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,744,847 number of insertions = 18,567 mapped reads with insertion percentage = 0.59% number of deletions = 68,432 mapped reads with deletion percentage = 2.16% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0723X std coverageData = 0.7817X There is a 4.01% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 13129114 0.05267434820152364 0.8848025268664552 chr2 243199373 14166820 0.058251877154305 0.7213856039823303 chr3 198022430 14951999 0.0755065928642528 0.44416528778589914 chr4 191154276 7833116 0.040977979482917766 0.4464168628791789 chr5 180915260 15325547 0.08471119020031809 0.47313895651760535 chr6 171115067 37132193 0.21700130591071795 1.1088724645135521 chr7 159138663 19504222 0.12256117798350487 1.5740257488545648 chr8 146364022 10008472 0.06838068442803519 1.2549551812933246 chr9 141213431 11600657 0.08214981335592646 0.7299962126202757 chr10 135534747 14282404 0.10537817287547672 0.9078349088200752 chr11 135006516 13867329 0.10271599779672856 0.7557382891906804 chr12 133851895 3173535 0.023709301986348418 0.2833033419778469 chr13 115169878 8156200 0.07081886463403217 0.4293703184954655 chr14 107349540 11705865 0.10904438901182063 0.5809871542684961 chr15 102531392 5990878 0.058429695365883653 0.3843998500102265 chr16 90354753 5396371 0.05972426265168364 0.4987330409627905 chr17 81195210 2134861 0.026292942650188354 0.4155523858678174 chr18 78077248 2356349 0.030179713813683597 1.3808464935007443 chr19 59128983 1441921 0.02438602740723614 0.6542244572711535 chr20 63025520 1671645 0.026523303576075217 0.2912574265233324 chr21 48129895 4566937 0.09488774076901685 0.5859956720454854 chr22 51304566 1325336 0.02583271048428711 0.24366227306722354 chrMT 16571 253382 15.290688552290145 11.210649281239439 chrX 155270560 3184795 0.020511261117368288 0.29504504630905154 chrY 59373566 530611 0.008936822154155269 0.3732272089810599