BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504632.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 581,613,740 number of mapped reads = 483,581,890 (83.14%) number of supplementary alignments = 4,159,930 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 245,815,731 number of mapped paired reads (second in pair) = 237,766,159 number of mapped paired reads (both in pair) = 460,102,776 number of mapped paired reads (singletons) = 23,479,114 number of mapped bases = 45,339,323,969 bp number of sequenced bases = 45,302,864,319 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,545,809 duplication rate = 22.86% >>>>>>> Insert size mean insert size = 103,120.0235 std insert size = 2,987,785.7585 median insert size = 353 >>>>>>> Mapping quality mean mapping quality = 51.4555 >>>>>>> ACTG content number of A's = 12,313,189,241 bp (27.18%) number of C's = 10,285,277,516 bp (22.7%) number of T's = 12,460,136,294 bp (27.5%) number of G's = 10,192,901,932 bp (22.5%) number of N's = 51,359,336 bp (0.11%) GC percentage = 45.2% >>>>>>> Mismatches and indels general error rate = 0.0269 number of mismatches = 1,172,078,239 number of insertions = 12,343,258 mapped reads with insertion percentage = 2.38% number of deletions = 11,308,582 mapped reads with deletion percentage = 2.18% homopolymer indels = 33.12% >>>>>>> Coverage mean coverageData = 14.6459X std coverageData = 303.3744X There is a 87.07% of reference with a coverageData >= 1X There is a 81.83% of reference with a coverageData >= 2X There is a 76.23% of reference with a coverageData >= 3X There is a 70.83% of reference with a coverageData >= 4X There is a 65.67% of reference with a coverageData >= 5X There is a 60.87% of reference with a coverageData >= 6X There is a 56.42% of reference with a coverageData >= 7X There is a 52.31% of reference with a coverageData >= 8X There is a 48.52% of reference with a coverageData >= 9X There is a 45.03% of reference with a coverageData >= 10X There is a 41.81% of reference with a coverageData >= 11X There is a 38.84% of reference with a coverageData >= 12X There is a 36.09% of reference with a coverageData >= 13X There is a 33.55% of reference with a coverageData >= 14X There is a 31.2% of reference with a coverageData >= 15X There is a 29.01% of reference with a coverageData >= 16X There is a 26.99% of reference with a coverageData >= 17X There is a 25.11% of reference with a coverageData >= 18X There is a 23.37% of reference with a coverageData >= 19X There is a 21.75% of reference with a coverageData >= 20X There is a 20.24% of reference with a coverageData >= 21X There is a 18.84% of reference with a coverageData >= 22X There is a 17.55% of reference with a coverageData >= 23X There is a 16.34% of reference with a coverageData >= 24X There is a 15.22% of reference with a coverageData >= 25X There is a 14.18% of reference with a coverageData >= 26X There is a 13.22% of reference with a coverageData >= 27X There is a 12.32% of reference with a coverageData >= 28X There is a 11.49% of reference with a coverageData >= 29X There is a 10.72% of reference with a coverageData >= 30X There is a 10% of reference with a coverageData >= 31X There is a 9.34% of reference with a coverageData >= 32X There is a 8.72% of reference with a coverageData >= 33X There is a 8.15% of reference with a coverageData >= 34X There is a 7.61% of reference with a coverageData >= 35X There is a 7.12% of reference with a coverageData >= 36X There is a 6.66% of reference with a coverageData >= 37X There is a 6.23% of reference with a coverageData >= 38X There is a 5.84% of reference with a coverageData >= 39X There is a 5.47% of reference with a coverageData >= 40X There is a 5.12% of reference with a coverageData >= 41X There is a 4.81% of reference with a coverageData >= 42X There is a 4.51% of reference with a coverageData >= 43X There is a 4.23% of reference with a coverageData >= 44X There is a 3.98% of reference with a coverageData >= 45X There is a 3.74% of reference with a coverageData >= 46X There is a 3.52% of reference with a coverageData >= 47X There is a 3.31% of reference with a coverageData >= 48X There is a 3.12% of reference with a coverageData >= 49X There is a 2.94% of reference with a coverageData >= 50X There is a 2.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3207410434 12.868214414599192 103.30214555969873 chr2 243199373 3425593942 14.085537720526936 312.03445403722765 chr3 198022430 2348086965 11.857681804025939 35.69429681210483 chr4 191154276 3273017291 17.122385956984818 764.1886995922907 chr5 180915260 2821688251 15.596739882528428 43.68094164439395 chr6 171115067 1359924518 7.947427084255532 31.378251137144066 chr7 159138663 2139481079 13.444131291966428 49.41565066952175 chr8 146364022 2533136188 17.30709605670716 229.7378435322557 chr9 141213431 1190165304 8.428131060706258 146.61177038416542 chr10 135534747 3374434921 24.897194230199876 750.0013000832374 chr11 135006516 1846758192 13.679030069926403 35.82745903517825 chr12 133851895 1723757086 12.878092506646992 31.648429666835735 chr13 115169878 709798165 6.163053893310541 15.269943278812418 chr14 107349540 1170380910 10.902523755574547 36.9487170231955 chr15 102531392 1546742178 15.085547438973617 25.163748587973956 chr16 90354753 2388526939 26.434989413340546 307.8806631369927 chr17 81195210 1440951416 17.746753977235848 98.16984174901333 chr18 78077248 753673744 9.652924037486567 388.9258349993453 chr19 59128983 1722760973 29.135643564172245 62.646525132309954 chr20 63025520 1324784324 21.019807912731224 208.52525853878473 chr21 48129895 859472032 17.857342759629955 277.774340431826 chr22 51304566 784263820 15.286433180235848 40.34551959727835 chrMT 16571 15134013 913.28302456098 425.8650149378863 chrX 155270560 2645200938 17.036075209621192 34.30054841966539 chrY 59373566 734180346 12.365441314405809 711.3606827541234