BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716354.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,257,310 number of mapped reads = 1,168,989 (92.98%) number of supplementary alignments = 23,454 (1.87%) number of secondary alignments = 0 number of mapped bases = 91,750,571 bp number of sequenced bases = 91,707,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,200 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3227 >>>>>>> ACTG content number of A's = 22,799,547 bp (24.86%) number of C's = 18,824,253 bp (20.53%) number of T's = 28,308,124 bp (30.87%) number of G's = 21,768,408 bp (23.74%) number of N's = 6,681 bp (0.01%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 624,878 number of insertions = 8,200 mapped reads with insertion percentage = 0.69% number of deletions = 23,045 mapped reads with deletion percentage = 1.94% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2768X There is a 2.66% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 7235414 0.029028669902491436 0.4884259963342996 chr2 243199373 7892570 0.032453085312847414 0.3076239802014009 chr3 198022430 6135889 0.030985828221580757 0.18974674678079329 chr4 191154276 5490314 0.028721900000814003 0.22374827689594748 chr5 180915260 5713846 0.03158299637078708 0.19249506401364597 chr6 171115067 5327576 0.031134464623153262 0.20356759208537348 chr7 159138663 5119288 0.03216872571060874 0.36894716642570585 chr8 146364022 4765421 0.032558691233560116 0.3368099269765676 chr9 141213431 3642503 0.025794309891103772 0.2500730427073487 chr10 135534747 4040256 0.029809743179732354 0.2879216292026852 chr11 135006516 4242366 0.03142341662975734 0.25666998820614934 chr12 133851895 4238140 0.031662906229306655 0.19314281660899088 chr13 115169878 2952781 0.02563848335412841 0.17154007766738702 chr14 107349540 2820897 0.026277681301661842 0.18651175203571235 chr15 102531392 2678184 0.02612062459856197 0.17511697537006315 chr16 90354753 2724809 0.030156786550011375 0.1995722677387735 chr17 81195210 2594080 0.03194868268706984 0.2073310744939918 chr18 78077248 2479108 0.03175199002915677 0.400247646896519 chr19 59128983 1907648 0.03226248623285132 0.35462633325065857 chr20 63025520 1833673 0.029094135201105837 0.1917426070008384 chr21 48129895 1238615 0.02573483694489672 0.19792663597588903 chr22 51304566 1164167 0.022691294182276098 0.1641336889172481 chrMT 16571 12526 0.7558988594532617 1.0200792127892833 chrX 155270560 5217232 0.033600909277328554 0.22125212588074394 chrY 59373566 283268 0.004770944699531775 0.15713393194875705