BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716203.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 = 5,441,455 number of mapped reads = 4,983,823 (91.59%) number of supplementary alignments = 116,998 (2.15%) number of secondary alignments = 0 number of mapped bases = 362,170,169 bp number of sequenced bases = 362,052,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,267 duplication rate = 4.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0345 >>>>>>> ACTG content number of A's = 93,533,634 bp (25.83%) number of C's = 75,894,184 bp (20.96%) number of T's = 105,846,123 bp (29.23%) number of G's = 86,739,168 bp (23.96%) number of N's = 39,674 bp (0.01%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 2,592,013 number of insertions = 25,327 mapped reads with insertion percentage = 0.5% number of deletions = 69,427 mapped reads with deletion percentage = 1.37% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.117X std coverageData = 0.7978X There is a 8.43% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 28960351 0.11618968443813828 0.9090564904096041 chr2 243199373 30677920 0.12614308837054444 1.2045860952002736 chr3 198022430 24467995 0.12356173490043527 0.46307117681819204 chr4 191154276 23458608 0.12272081216744532 0.5276306779505218 chr5 180915260 21910590 0.12110968416926245 0.4690916507208758 chr6 171115067 20766103 0.12135753656339333 0.5787411890921207 chr7 159138663 19961364 0.1254337797220277 1.1797674481221385 chr8 146364022 18418336 0.12583923117390147 1.0291387224767594 chr9 141213431 15409481 0.10912192197922023 0.854064916319676 chr10 135534747 17315115 0.12775406590016358 0.7717017546068287 chr11 135006516 16433751 0.1217256135992725 0.8866106808458609 chr12 133851895 16382973 0.12239627238747722 0.48337004034025655 chr13 115169878 11493383 0.09979504363111334 0.41320941902330477 chr14 107349540 11129365 0.10367408188241888 0.5973996055743396 chr15 102531392 9882244 0.09638261811563038 0.4154287962675842 chr16 90354753 10735113 0.1188107171296235 0.55318260939368 chr17 81195210 9806106 0.12077197657349491 0.539637174593381 chr18 78077248 9813400 0.12568834393343373 1.7128544476529632 chr19 59128983 7156841 0.12103778277397398 0.8395821441747888 chr20 63025520 7667451 0.12165629097546518 0.5034776745293176 chr21 48129895 4698461 0.09762042904934656 0.4849875861859808 chr22 51304566 4141404 0.0807219380824701 0.37455662524324923 chrMT 16571 103514 6.246696035242291 6.348734785524022 chrX 155270560 20473734 0.13185844116231693 0.7113867693789202 chrY 59373566 906566 0.015268848766806427 0.3634588372901304