BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038447.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,499,644 number of mapped reads = 14,603,532 (94.22%) number of supplementary alignments = 209,120 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,377,262 number of mapped paired reads (second in pair) = 7,226,270 number of mapped paired reads (both in pair) = 14,430,572 number of mapped paired reads (singletons) = 172,960 number of mapped bases = 2,108,077,595 bp number of sequenced bases = 2,106,653,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,072,443 duplication rate = 10.01% >>>>>>> Insert size mean insert size = 79,256.3214 std insert size = 2,737,626.3358 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.948 >>>>>>> ACTG content number of A's = 608,999,334 bp (28.91%) number of C's = 440,202,566 bp (20.9%) number of T's = 607,358,701 bp (28.83%) number of G's = 450,048,899 bp (21.36%) number of N's = 44,309 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 27,923,687 number of insertions = 367,894 mapped reads with insertion percentage = 2.34% number of deletions = 731,643 mapped reads with deletion percentage = 4.8% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.681X std coverageData = 7.7201X There is a 23.61% of reference with a coverageData >= 1X There is a 14.48% of reference with a coverageData >= 2X There is a 8.58% of reference with a coverageData >= 3X There is a 5.66% of reference with a coverageData >= 4X There is a 3.68% of reference with a coverageData >= 5X There is a 2.5% of reference with a coverageData >= 6X There is a 1.71% of reference with a coverageData >= 7X There is a 1.2% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167259341 0.6710488436456092 7.242918870831934 chr2 243199373 195637233 0.8044314859315036 11.634274223121649 chr3 198022430 144998994 0.7322352018405188 1.793740952167654 chr4 191154276 137420418 0.718897954445968 4.62710005514575 chr5 180915260 132726657 0.7336399207009956 1.949328472065161 chr6 171115067 127849543 0.7471553805370044 10.733542851612881 chr7 159138663 112394885 0.7062701349954159 8.442449622219584 chr8 146364022 110227033 0.7531019679139455 2.9177921499219472 chr9 141213431 94667721 0.670387514343448 17.269787389606368 chr10 135534747 107551625 0.7935354392921838 11.048305443000716 chr11 135006516 100907654 0.7474280278442265 5.555313863925263 chr12 133851895 91406950 0.6828961965760739 1.792642224425131 chr13 115169878 65437643 0.5681836617036271 1.5657677433752368 chr14 107349540 63202559 0.588754819070487 1.8061894575710513 chr15 102531392 60827125 0.593253673957728 1.6281522414108445 chr16 90354753 67701877 0.7492896029498304 9.221321233679669 chr17 81195210 52022378 0.6407074752316054 7.577685110245377 chr18 78077248 62556265 0.8012099120091938 14.91652411562819 chr19 59128983 29312507 0.49573839279461307 4.172905136101562 chr20 63025520 46002808 0.7299076310675422 2.233244138327092 chr21 48129895 27879173 0.5792485730542317 2.997876022079662 chr22 51304566 20823868 0.4058872264897436 1.5552765228584835 chrMT 16571 2767009 166.97899945688252 99.67105546861809 chrX 155270560 64895735 0.4179526047951395 2.0167407768411953 chrY 59373566 21600594 0.36380826443875713 7.914959970387822