BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237251.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 = 2,389,023 number of mapped reads = 1,753,829 (73.41%) number of supplementary alignments = 16,368 (0.69%) number of secondary alignments = 0 number of mapped bases = 115,982,214 bp number of sequenced bases = 115,938,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,227 duplication rate = 9.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6062 >>>>>>> ACTG content number of A's = 31,284,749 bp (26.98%) number of C's = 21,505,389 bp (18.55%) number of T's = 36,708,328 bp (31.66%) number of G's = 26,438,560 bp (22.8%) number of N's = 1,663 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 948,401 number of insertions = 8,973 mapped reads with insertion percentage = 0.51% number of deletions = 26,353 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.4112X There is a 2% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 8711334 0.034950099482400084 0.6770111819084728 chr2 243199373 15218754 0.06257727481887874 0.5683465554006533 chr3 198022430 6334769 0.03199015889260626 0.309368254809669 chr4 191154276 8018605 0.041948342290810174 0.3749141552796834 chr5 180915260 6936038 0.038338601177147796 0.3438378268685278 chr6 171115067 7519925 0.043946597642392296 0.41388003247121596 chr7 159138663 6725898 0.042264386750566076 0.4207189965651477 chr8 146364022 5283056 0.03609531856127867 0.36828450638292787 chr9 141213431 6165926 0.0436638778360962 0.3913469497461884 chr10 135534747 4419176 0.0326054838173712 0.36780667113787235 chr11 135006516 4755880 0.03522704044892174 0.3441487741603094 chr12 133851895 4768698 0.03562667528913207 0.3271394030095456 chr13 115169878 3528452 0.03063693442481549 0.3051763649083796 chr14 107349540 2056914 0.019160901853887777 0.24850426848082144 chr15 102531392 3405811 0.03321725116147843 0.34853259838013595 chr16 90354753 3628983 0.040163719998216364 0.36048322743380606 chr17 81195210 2222327 0.02737017368389096 0.2882631799236244 chr18 78077248 3996917 0.05119182735539039 0.4939202496970688 chr19 59128983 1782871 0.03015223515682656 0.4291739916218689 chr20 63025520 2631769 0.041757196132614215 0.37223564926306335 chr21 48129895 1273742 0.026464674398313147 0.2821786260197772 chr22 51304566 1426482 0.027804191930987196 0.29480653441849886 chrMT 16571 176481 10.64999094804176 7.224879678183784 chrX 155270560 4747329 0.030574559658959173 0.3273910255580936 chrY 59373566 246077 0.00414455483438539 0.11627808349219705