BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068109.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 = 3,888,026 number of mapped reads = 3,662,064 (94.19%) number of supplementary alignments = 17,820 (0.46%) number of secondary alignments = 0 number of mapped bases = 236,489,161 bp number of sequenced bases = 236,396,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,446,588 duplication rate = 18.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3215 >>>>>>> ACTG content number of A's = 62,288,327 bp (26.35%) number of C's = 42,805,629 bp (18.11%) number of T's = 76,601,924 bp (32.4%) number of G's = 54,674,206 bp (23.13%) number of N's = 26,708 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,191,764 number of insertions = 15,770 mapped reads with insertion percentage = 0.43% number of deletions = 52,051 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.0764X std coverageData = 0.954X There is a 1.87% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 28495997 0.11432668406471092 1.5416562525693502 chr2 243199373 22823983 0.09384885626329308 1.0444673084317235 chr3 198022430 15510466 0.07832681378569084 0.7903712206198256 chr4 191154276 10605205 0.055479820917006324 0.7467454648790481 chr5 180915260 12153650 0.06717868907244198 0.7413408928799204 chr6 171115067 15394442 0.08996543828603942 0.8656668363344149 chr7 159138663 21415179 0.13456930324970745 1.164450294497791 chr8 146364022 8330609 0.05691705438376106 1.0681131407501574 chr9 141213431 8537347 0.06045704675216056 0.7389214317800651 chr10 135534747 7960459 0.058733713503003035 1.2627656131626763 chr11 135006516 10356927 0.07671427503543607 0.8601150428536727 chr12 133851895 8825297 0.06593329888979159 0.7363021234374247 chr13 115169878 5927371 0.051466330458386 0.6441457288548637 chr14 107349540 5617871 0.05233251115933985 0.6477064829007245 chr15 102531392 4664148 0.04548995101909862 0.5964590171209209 chr16 90354753 5515747 0.061045454908166256 0.7073359842426128 chr17 81195210 7316088 0.09010492121394846 0.87468836811673 chr18 78077248 5787611 0.07412672895438117 0.9629094930631964 chr19 59128983 4732057 0.08002939945711564 1.0933749657937961 chr20 63025520 3713623 0.05892252852495307 0.6962469152569973 chr21 48129895 4034726 0.08382993563563769 0.824653503625068 chr22 51304566 3114253 0.06070128339064402 0.7064872114481521 chrMT 16571 340843 20.568644016655604 27.900022573304252 chrX 155270560 14760393 0.0950624059061808 1.013877651616202 chrY 59373566 554869 0.009345387811134672 0.24645671122667373