BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,310,772 number of mapped reads = 1,994,415 (86.31%) number of supplementary alignments = 25,261 (1.09%) number of secondary alignments = 0 number of mapped bases = 131,962,143 bp number of sequenced bases = 131,914,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,101 duplication rate = 10.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1983 >>>>>>> ACTG content number of A's = 35,905,800 bp (27.22%) number of C's = 25,196,668 bp (19.1%) number of T's = 40,725,498 bp (30.87%) number of G's = 30,038,357 bp (22.77%) number of N's = 48,634 bp (0.04%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,004,572 number of insertions = 9,061 mapped reads with insertion percentage = 0.45% number of deletions = 27,439 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.4697X There is a 2.16% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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% 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 12162751 0.048797274611404075 0.7433860336541908 chr2 243199373 9826303 0.040404310581836904 0.4597967015209738 chr3 198022430 10414222 0.052591123136909286 0.3945615185895433 chr4 191154276 7173533 0.03752745243323775 0.3346803821870729 chr5 180915260 4135612 0.022859387317576196 0.2539800693554538 chr6 171115067 6433875 0.037599698920726836 0.3445222978355074 chr7 159138663 9238348 0.05805219062321769 0.6481269533603882 chr8 146364022 12140699 0.08294865660360166 0.829637162691298 chr9 141213431 2618725 0.018544447092996415 0.31849179810593997 chr10 135534747 7228441 0.05333275163748231 0.4264990155133331 chr11 135006516 6879958 0.050960192173242956 0.5547254837250956 chr12 133851895 5571751 0.041626239210135946 0.34585610764279756 chr13 115169878 2960254 0.025703370112105182 0.27425764270159464 chr14 107349540 4728991 0.04405227074098315 0.36103293872126235 chr15 102531392 3027617 0.029528683273899178 0.2883531372929897 chr16 90354753 3808335 0.04214869581902349 0.35615379069641917 chr17 81195210 4125392 0.05080831738719562 0.44413596243959047 chr18 78077248 2265427 0.02901520043329396 0.55340028788576 chr19 59128983 3261608 0.055160901380630886 0.5356604131517935 chr20 63025520 3426047 0.054359678428674604 0.4053306671190827 chr21 48129895 1470024 0.03054284660292735 0.3031869512233217 chr22 51304566 1480768 0.02886230438047171 0.28485457408775444 chrMT 16571 71596 4.320560014483133 5.423739974640264 chrX 155270560 7153998 0.046074400710604764 0.3956799003183955 chrY 59373566 357868 0.006027396097448484 0.14124988570106595