BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081207.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,828,064 number of mapped reads = 4,631,021 (79.46%) number of supplementary alignments = 38,502 (0.66%) number of secondary alignments = 0 number of mapped bases = 298,636,600 bp number of sequenced bases = 298,531,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 428,392 duplication rate = 6.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7657 >>>>>>> ACTG content number of A's = 84,175,525 bp (28.2%) number of C's = 54,537,120 bp (18.27%) number of T's = 95,628,479 bp (32.03%) number of G's = 64,023,916 bp (21.45%) number of N's = 166,061 bp (0.06%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,064,247 number of insertions = 22,647 mapped reads with insertion percentage = 0.49% number of deletions = 67,700 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0965X std coverageData = 1.0847X There is a 6.89% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 29010740 0.11639184642191924 2.5350824730505486 chr2 243199373 18136347 0.07457398749132466 0.75096983726586 chr3 198022430 19223630 0.09707804312875061 0.4304794749351875 chr4 191154276 12790300 0.06691087569498053 0.3476799819115815 chr5 180915260 21773911 0.12035419787142333 0.46647676764150736 chr6 171115067 20939613 0.1223715326015096 0.6834689976103255 chr7 159138663 19232298 0.12085245431526592 1.4860214499701507 chr8 146364022 18066958 0.12343851824459975 1.752673024378628 chr9 141213431 14396794 0.10195059986893173 0.7341686129303644 chr10 135534747 8893522 0.06561802192318993 0.9711310840748522 chr11 135006516 15586264 0.11544823510592629 0.7266166293390185 chr12 133851895 8180593 0.061116751466238114 0.36043660715562226 chr13 115169878 10192346 0.08849836586611648 0.3908703500035608 chr14 107349540 10378799 0.09668228666839188 1.2535486734873433 chr15 102531392 9627341 0.09389652097964299 0.4016573679383039 chr16 90354753 8395191 0.09291366221763674 0.46238898391807215 chr17 81195210 4132242 0.05089268196978615 0.3794478645486514 chr18 78077248 9360232 0.11988424592014309 1.2383179953915793 chr19 59128983 6166157 0.1042831567050629 1.7953889284698274 chr20 63025520 6294879 0.09987825566532414 0.4369571682452349 chr21 48129895 4341612 0.09020613903271553 0.43514973204291907 chr22 51304566 1639156 0.03194951498079138 0.22592195880590393 chrMT 16571 318941 19.246937420795366 12.101760679306384 chrX 155270560 20854178 0.13430864163818304 0.5671289452443599 chrY 59373566 704556 0.011866492910329826 0.18270541938794743