BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671995.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 27,239,810 number of mapped reads = 26,992,262 (99.09%) number of supplementary alignments = 633,909 (2.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,505,507 number of mapped paired reads (second in pair) = 13,486,755 number of mapped paired reads (both in pair) = 26,933,926 number of mapped paired reads (singletons) = 58,336 number of mapped bases = 3,564,436,581 bp number of sequenced bases = 3,563,135,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,380,635 duplication rate = 46.51% >>>>>>> Insert size mean insert size = 152,642.5567 std insert size = 3,939,430.6711 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.1244 >>>>>>> ACTG content number of A's = 945,059,024 bp (26.52%) number of C's = 764,324,750 bp (21.45%) number of T's = 1,013,847,207 bp (28.45%) number of G's = 839,899,517 bp (23.57%) number of N's = 5,328 bp (0%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 30,743,348 number of insertions = 361,300 mapped reads with insertion percentage = 1.28% number of deletions = 722,661 mapped reads with deletion percentage = 2.62% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 1.1514X std coverageData = 53.5964X There is a 15.38% of reference with a coverageData >= 1X There is a 10.54% of reference with a coverageData >= 2X There is a 6% of reference with a coverageData >= 3X There is a 4.37% of reference with a coverageData >= 4X There is a 2.68% of reference with a coverageData >= 5X There is a 2.01% of reference with a coverageData >= 6X There is a 1.32% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.71% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.42% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 360520476 1.446417563790142 65.15829780337916 chr2 243199373 426996531 1.755746841501931 70.38361661546226 chr3 198022430 88463045 0.4467324484403105 8.954058941294004 chr4 191154276 214135013 1.1202208890163672 57.307619011779906 chr5 180915260 155991949 0.8622376520366496 41.97159156397549 chr6 171115067 250708171 1.4651437503162712 65.2146999908182 chr7 159138663 230786128 1.4502203528001238 79.66829815076694 chr8 146364022 67465714 0.4609446575607221 6.208852006239191 chr9 141213431 177998537 1.2604929696807665 64.94830039195793 chr10 135534747 162002193 1.1952816276699878 45.21781974404855 chr11 135006516 222269956 1.646364653984553 66.08728892712601 chr12 133851895 168850101 1.2614696340309564 50.020561019289225 chr13 115169878 110895373 0.9628852172614093 44.133086656046714 chr14 107349540 102605906 0.9558113243894664 45.68099092450114 chr15 102531392 119994264 1.17031732096254 55.979374756022104 chr16 90354753 86589102 0.9583237087704728 28.954359213492697 chr17 81195210 166839970 2.0548006464913384 69.77322405285389 chr18 78077248 44907022 0.5751614349932006 23.45432221435103 chr19 59128983 55029036 0.9306609586029917 36.88454740549937 chr20 63025520 64334084 1.0207624467041287 42.31975625537235 chr21 48129895 38712864 0.8043413350475832 45.399850472395464 chr22 51304566 18119530 0.3531757777660569 5.936490364543078 chrMT 16571 125690 7.584937541488142 24.15859586339605 chrX 155270560 217101581 1.3982147098587137 59.238115046528485 chrY 59373566 12994345 0.21885741206785525 7.17513748569174