BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238259.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 = 1,632,892 number of mapped reads = 1,287,712 (78.86%) number of supplementary alignments = 14,102 (0.86%) number of secondary alignments = 0 number of mapped bases = 81,954,873 bp number of sequenced bases = 81,904,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,352 duplication rate = 8.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3488 >>>>>>> ACTG content number of A's = 23,170,396 bp (28.29%) number of C's = 15,507,844 bp (18.93%) number of T's = 25,353,803 bp (30.96%) number of G's = 17,852,770 bp (21.8%) number of N's = 19,606 bp (0.02%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 808,265 number of insertions = 6,952 mapped reads with insertion percentage = 0.54% number of deletions = 30,892 mapped reads with deletion percentage = 2.37% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2845X There is a 1.71% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 6148190 0.0246666988243933 0.3539442260933013 chr2 243199373 7112200 0.02924431881656208 0.34095141599987944 chr3 198022430 5425043 0.02739610356261157 0.23883052622684087 chr4 191154276 5078323 0.026566619937918628 0.24537716401716744 chr5 180915260 5262772 0.02908970752384293 0.2474528612089835 chr6 171115067 4879373 0.028515156996665875 0.2722283313708503 chr7 159138663 5152947 0.032380233080128364 0.377583784254011 chr8 146364022 4154109 0.02838203639962832 0.3543119864632264 chr9 141213431 3242384 0.0229608754425066 0.257507009657972 chr10 135534747 3551673 0.026204888994259164 0.2717713007927326 chr11 135006516 3575537 0.02648418095612511 0.26168952562967357 chr12 133851895 3604701 0.026930518988916817 0.23871675721790497 chr13 115169878 3046768 0.026454556112319578 0.2424770661705348 chr14 107349540 2908323 0.027092086281878803 0.2735026697098047 chr15 102531392 2324312 0.022669271865537532 0.2629264633351916 chr16 90354753 2337043 0.025865191618641245 0.23646513691293006 chr17 81195210 2102088 0.02588931046548189 0.2355768507508436 chr18 78077248 2100890 0.026907838759890716 0.38927461394510143 chr19 59128983 1388002 0.023474139577201927 0.2863073637153799 chr20 63025520 1578152 0.02503988860385444 0.22953129177303364 chr21 48129895 1008967 0.02096341577308656 0.20932038158015684 chr22 51304566 913581 0.017807011563064388 0.18698667853004292 chrMT 16571 13726 0.8283145253756563 1.4360585156467671 chrX 155270560 4825485 0.031077913288906796 0.26856517346799097 chrY 59373566 220284 0.0037101359214300857 0.1033177945847382