BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716535.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 = 1,196,373 number of mapped reads = 1,110,416 (92.82%) number of supplementary alignments = 22,920 (1.92%) number of secondary alignments = 0 number of mapped bases = 87,640,098 bp number of sequenced bases = 87,601,074 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,671 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.297 >>>>>>> ACTG content number of A's = 22,923,214 bp (26.17%) number of C's = 17,536,286 bp (20.02%) number of T's = 26,610,706 bp (30.38%) number of G's = 20,524,648 bp (23.43%) number of N's = 6,220 bp (0.01%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 575,383 number of insertions = 7,238 mapped reads with insertion percentage = 0.64% number of deletions = 20,612 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.2861X There is a 2.54% 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 8512807 0.03415360397437084 0.5923766749858647 chr2 243199373 7190271 0.029565335269182622 0.29559542537654243 chr3 198022430 5592021 0.02823933127171503 0.17945011911853812 chr4 191154276 5591046 0.029248867025082923 0.21272084236577854 chr5 180915260 5127456 0.02834175513994784 0.18208084695057272 chr6 171115067 4858999 0.028396090918165612 0.19328569677219096 chr7 159138663 4584626 0.02880900161892148 0.3138630428177944 chr8 146364022 4345545 0.02968998077956617 0.31618482005975196 chr9 141213431 3564964 0.025245219061351184 0.23405742796882884 chr10 135534747 3990484 0.029442516316498527 0.27964825323869963 chr11 135006516 4841157 0.03585869144271525 0.30100676635890994 chr12 133851895 3778124 0.028226152494889967 0.18183844973896826 chr13 115169878 3109391 0.02699830071887373 0.17766920513910497 chr14 107349540 2527452 0.023544134422932787 0.17778294421026533 chr15 102531392 2427506 0.023675734354606248 0.16473121916734235 chr16 90354753 1919592 0.021245058353488055 0.17107034378805372 chr17 81195210 2886589 0.03555122278764967 0.24205240188413785 chr18 78077248 2274437 0.029130598967832474 0.37358889731016914 chr19 59128983 1643388 0.027793273562645243 0.4212281876167901 chr20 63025520 1788540 0.02837802845577474 0.1851135737626654 chr21 48129895 1141448 0.023715987745246483 0.18263565743092905 chr22 51304566 954026 0.018595342956414445 0.14709391117399814 chrMT 16571 44629 2.6931989620421217 2.299048658928539 chrX 155270560 4691573 0.030215470337712443 0.21265637761217643 chrY 59373566 254027 0.004278452805074905 0.1409675488666965