BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,037,410 number of mapped reads = 1,986,457 (97.5%) number of supplementary alignments = 196,229 (9.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 995,475 number of mapped paired reads (second in pair) = 990,982 number of mapped paired reads (both in pair) = 1,953,124 number of mapped paired reads (singletons) = 33,333 number of mapped bases = 234,320,894 bp number of sequenced bases = 234,191,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,493,563 duplication rate = 62.99% >>>>>>> Insert size mean insert size = 999,204.9024 std insert size = 9,339,771.8547 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.154 >>>>>>> ACTG content number of A's = 70,822,676 bp (30.24%) number of C's = 45,532,412 bp (19.44%) number of T's = 70,694,975 bp (30.19%) number of G's = 47,138,224 bp (20.13%) number of N's = 2,920 bp (0%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,366,400 number of insertions = 25,439 mapped reads with insertion percentage = 1.24% number of deletions = 53,763 mapped reads with deletion percentage = 2.64% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0757X std coverageData = 1.2104X There is a 1.75% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 18627698 0.0747348107911033 0.9056580941083238 chr2 243199373 22365885 0.09196522476231878 3.21429457625111 chr3 198022430 15997708 0.0807873532306416 0.8033462836747913 chr4 191154276 16191954 0.08470620871698419 0.9109588566297322 chr5 180915260 14891957 0.0823145432839662 0.8008528226396274 chr6 171115067 13405916 0.07834445110552421 0.826003569157612 chr7 159138663 12743499 0.08007795691987182 0.8943878730810896 chr8 146364022 12086420 0.08257780727015003 1.0587188658766458 chr9 141213431 9942582 0.07040818943064983 0.8522254214655773 chr10 135534747 11635780 0.08585089991719982 1.08638878271786 chr11 135006516 10332499 0.07653333562063035 0.7709803540535216 chr12 133851895 11012097 0.08227075903557436 0.7956829835704026 chr13 115169878 8136672 0.07064930640978885 0.7542275481848042 chr14 107349540 7534048 0.07018239668283628 0.7374004402553498 chr15 102531392 7226497 0.07048082405825525 0.735698697276078 chr16 90354753 6685772 0.07399469068328923 0.8113624434014965 chr17 81195210 5834994 0.07186377127419216 0.7603627364669916 chr18 78077248 6552450 0.08392265567556889 1.0379528543867182 chr19 59128983 3823250 0.06465949194492318 0.7591954036204103 chr20 63025520 4972897 0.07890291107475195 0.7947761968767526 chr21 48129895 3427293 0.07120923492561121 0.8365911009331111 chr22 51304566 2683194 0.05229932166271516 0.6378190187386391 chrMT 16571 364214 21.978999456882505 18.675555772798965 chrX 155270560 6133589 0.039502588256267 0.5545192608470955 chrY 59373566 1712029 0.028834869039194983 0.5776678059991142