BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716132.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 = 991,713 number of mapped reads = 862,407 (86.96%) number of supplementary alignments = 4,876 (0.49%) number of secondary alignments = 0 number of mapped bases = 49,339,578 bp number of sequenced bases = 49,325,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,641 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2746 >>>>>>> ACTG content number of A's = 13,182,558 bp (26.73%) number of C's = 8,912,963 bp (18.07%) number of T's = 15,172,031 bp (30.76%) number of G's = 12,056,910 bp (24.44%) number of N's = 779 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 273,779 number of insertions = 4,184 mapped reads with insertion percentage = 0.48% number of deletions = 8,686 mapped reads with deletion percentage = 1% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1773X There is a 1.48% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3546638 0.014229204267458977 0.26068267025235586 chr2 243199373 4097329 0.016847613336568923 0.20398306316302645 chr3 198022430 2903973 0.014664869025190732 0.12669009917720625 chr4 191154276 3006327 0.01572722861820784 0.14306225518063315 chr5 180915260 2677039 0.014797198423173369 0.12852480528994267 chr6 171115067 2552769 0.014918434973350419 0.13746221634572192 chr7 159138663 3148853 0.019786850917554836 0.2243416113302157 chr8 146364022 2140491 0.014624434138602723 0.15621039984333507 chr9 141213431 2288871 0.016208592793131697 0.19328028622403198 chr10 135534747 1938512 0.014302693906234981 0.18424496493292886 chr11 135006516 1894413 0.014032011610461824 0.15717276765677365 chr12 133851895 3624663 0.027079653971279226 0.18471379862322174 chr13 115169878 1792990 0.015568220016695685 0.12998605560317456 chr14 107349540 1758997 0.016385696669030905 0.14871612769012424 chr15 102531392 1258514 0.012274426158185778 0.11665216904752886 chr16 90354753 1463947 0.016202213512774476 0.14264456223931862 chr17 81195210 1549173 0.01907961073073153 0.14826075224760424 chr18 78077248 1540863 0.019735109003841938 0.3260767573159904 chr19 59128983 920176 0.015562182085898551 0.22125615430157902 chr20 63025520 1436361 0.022790149133239995 0.1635933835290819 chr21 48129895 588897 0.012235576246322582 0.12952561141546348 chr22 51304566 510783 0.009955897492632527 0.10423169517167993 chrMT 16571 4082 0.2463339569126788 0.5127347419166257 chrX 155270560 2543052 0.016378198159393512 0.15251434228573038 chrY 59373566 151865 0.00255778809041047 0.07488332053073242