BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008826.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 = 1,464,237 number of mapped reads = 169,253 (11.56%) number of supplementary alignments = 1,910 (0.13%) number of secondary alignments = 0 number of mapped bases = 11,015,085 bp number of sequenced bases = 11,009,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,278 duplication rate = 6.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1128 >>>>>>> ACTG content number of A's = 3,056,357 bp (27.76%) number of C's = 1,986,478 bp (18.04%) number of T's = 3,566,837 bp (32.4%) number of G's = 2,384,899 bp (21.66%) number of N's = 14,495 bp (0.13%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 97,846 number of insertions = 832 mapped reads with insertion percentage = 0.49% number of deletions = 3,355 mapped reads with deletion percentage = 1.96% homopolymer indels = 45.4% >>>>>>> Coverage mean coverageData = 0.0036X std coverageData = 0.0958X There is a 0.24% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 539182 0.00216321226337085 0.1013349908687075 chr2 243199373 1238602 0.005092948985522261 0.12600357271670884 chr3 198022430 512669 0.0025889440908284985 0.07120635838637933 chr4 191154276 996401 0.005212548841962604 0.10858774172085425 chr5 180915260 914575 0.00505526731133681 0.1036297402102238 chr6 171115067 371242 0.002169545946529653 0.06752650312243832 chr7 159138663 332406 0.0020887821584877836 0.06416490504548869 chr8 146364022 1003958 0.006859322299847704 0.13163090171372485 chr9 141213431 473658 0.0033541993608242546 0.0837266170954916 chr10 135534747 308491 0.0022761026735085136 0.06693076380180456 chr11 135006516 312897 0.0023176436906200883 0.07772382498946293 chr12 133851895 696947 0.0052068519463247045 0.10966215258901153 chr13 115169878 408986 0.003551154234964111 0.08766840383360514 chr14 107349540 778866 0.007255420004594337 0.13815084631198823 chr15 102531392 208607 0.0020345671304257723 0.06613701785169193 chr16 90354753 244130 0.0027019054548242747 0.09610465947325247 chr17 81195210 182458 0.002247152264277659 0.0647421410126035 chr18 78077248 594514 0.007614433336584814 0.13222163929874858 chr19 59128983 156486 0.0026465193896536322 0.07368038482804878 chr20 63025520 113800 0.0018056177878421312 0.05547632593176927 chr21 48129895 85650 0.0017795592531419401 0.14902405549360737 chr22 51304566 97690 0.0019041190212972466 0.05889253053194514 chrMT 16571 12255 0.7395449882324543 1.1876892042722569 chrX 155270560 408171 0.0026287726404799466 0.08042988671367998 chrY 59373566 22444 3.780133401453435E-4 0.02761834115878968