BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004113.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 = 4,037,972 number of mapped reads = 3,579,835 (88.65%) number of supplementary alignments = 21,991 (0.54%) number of secondary alignments = 0 number of mapped bases = 244,308,333 bp number of sequenced bases = 244,201,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,705 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0399 >>>>>>> ACTG content number of A's = 67,579,081 bp (27.67%) number of C's = 46,111,348 bp (18.88%) number of T's = 77,219,178 bp (31.62%) number of G's = 53,257,954 bp (21.81%) number of N's = 33,490 bp (0.01%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,276,749 number of insertions = 19,773 mapped reads with insertion percentage = 0.55% number of deletions = 63,829 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.0789X std coverageData = 0.6361X There is a 5.91% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 15161795 0.06082951745183415 1.122881017244461 chr2 243199373 20382403 0.08380943893305186 0.7601761945842037 chr3 198022430 13058758 0.06594585269961589 0.32946942305257304 chr4 191154276 21718998 0.1136202571790756 0.462822244730259 chr5 180915260 12432666 0.06872093597853492 0.3328927350034116 chr6 171115067 16159896 0.09443876733543283 0.4699619416356274 chr7 159138663 9824867 0.06173777518791898 0.6359306860142608 chr8 146364022 16038294 0.10957811749666185 1.0949120498893283 chr9 141213431 3272656 0.023175245986339642 0.464354060349116 chr10 135534747 8296365 0.061212089029833806 0.6245327983369093 chr11 135006516 9130450 0.0676296987028389 0.5042286636623631 chr12 133851895 14668783 0.10958965504373322 0.42222498222508553 chr13 115169878 9710973 0.08431868791247656 0.3651941941522382 chr14 107349540 7672363 0.0714708512025296 0.3639308854876805 chr15 102531392 6695418 0.06530115186576224 0.32385411091273414 chr16 90354753 7920798 0.08766332414189655 0.4893004671593877 chr17 81195210 7516638 0.09257489450424478 0.4343363287955984 chr18 78077248 7603940 0.09738995923626817 1.2326860951039718 chr19 59128983 5284339 0.08936969201719569 0.7581119219292665 chr20 63025520 5912676 0.09381399788530106 0.4130498429397048 chr21 48129895 4026386 0.08365665455949987 0.4011936155367392 chr22 51304566 2997919 0.0584337659147141 0.3053856221164666 chrMT 16571 32550 1.964274938144952 1.951606058288402 chrX 155270560 18097073 0.11655186276136313 0.49175349297571735 chrY 59373566 691329 0.011643717003624139 0.2413447263946022