BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068153.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 = 4,049,545 number of mapped reads = 3,846,319 (94.98%) number of supplementary alignments = 39,656 (0.98%) number of secondary alignments = 0 number of mapped bases = 246,482,873 bp number of sequenced bases = 246,385,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 510,583 duplication rate = 10.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6517 >>>>>>> ACTG content number of A's = 64,246,847 bp (26.08%) number of C's = 45,069,509 bp (18.29%) number of T's = 79,196,329 bp (32.14%) number of G's = 57,844,000 bp (23.48%) number of N's = 28,901 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,355,955 number of insertions = 14,990 mapped reads with insertion percentage = 0.39% number of deletions = 56,690 mapped reads with deletion percentage = 1.46% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.0796X std coverageData = 0.8107X There is a 5.59% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 26711969 0.10716911714334304 1.6285633721632053 chr2 243199373 23628332 0.09715622087561879 1.3938206191683506 chr3 198022430 11719605 0.05918321979989843 0.32692989406511896 chr4 191154276 5794998 0.03031581673851753 0.2667043599767488 chr5 180915260 14313758 0.07911857739363722 0.3800704414272144 chr6 171115067 18716767 0.10938117448184735 0.5725327361735176 chr7 159138663 27925119 0.1754766470546507 1.383295127549652 chr8 146364022 8723241 0.05959962619775507 0.8045079729230655 chr9 141213431 4198368 0.029730656427432882 0.36745366523854334 chr10 135534747 13577816 0.10017959453600485 0.5284690253645624 chr11 135006516 10517932 0.07790684710358721 0.4531842507763333 chr12 133851895 12779219 0.09547282838244464 0.4190514204784403 chr13 115169878 5338841 0.04635622692940597 0.33454668275450034 chr14 107349540 4578959 0.04265466810570404 0.2922013540567557 chr15 102531392 3757522 0.03664752742262584 0.2780801104344638 chr16 90354753 6140132 0.0679558274040105 0.3631475539050949 chr17 81195210 6872498 0.08464166790134542 0.4097599420494356 chr18 78077248 4946874 0.06335871366777682 0.7918855254599292 chr19 59128983 6332815 0.10710170678903778 1.1251773313872502 chr20 63025520 3855103 0.061167333486498804 0.354426675692466 chr21 48129895 4182802 0.08690652659848935 0.4002103300072169 chr22 51304566 3639704 0.0709430813623879 0.35414015588220493 chrMT 16571 555075 33.49677146822763 20.027104341472025 chrX 155270560 17109293 0.11019019316990936 0.5297670051793104 chrY 59373566 566131 0.0095350681816888 0.21466602698047527