BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716819.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 = 483,082 number of mapped reads = 389,353 (80.6%) number of supplementary alignments = 1,861 (0.39%) number of secondary alignments = 0 number of mapped bases = 22,255,757 bp number of sequenced bases = 22,249,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,378 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6978 >>>>>>> ACTG content number of A's = 5,234,597 bp (23.53%) number of C's = 4,606,033 bp (20.7%) number of T's = 7,039,667 bp (31.64%) number of G's = 5,368,591 bp (24.13%) number of N's = 161 bp (0%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 118,710 number of insertions = 1,718 mapped reads with insertion percentage = 0.44% number of deletions = 4,212 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.0072X std coverageData = 0.0995X There is a 0.67% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 1840341 0.007383496147839086 0.11652827303778816 chr2 243199373 1907327 0.00784264768643133 0.12702974613920992 chr3 198022430 1450329 0.007324064248681324 0.09008302872716717 chr4 191154276 1348370 0.0070538312206000564 0.09474657584085668 chr5 180915260 1325565 0.007326993864420281 0.0900597203712687 chr6 171115067 1238917 0.007240256639703154 0.09217665272267767 chr7 159138663 1264565 0.007946309062556344 0.11530780293253354 chr8 146364022 1152076 0.00787130596889446 0.1058653540530455 chr9 141213431 912254 0.00646010789157867 0.08849167521811917 chr10 135534747 1072628 0.007914044359414342 0.10609838553810534 chr11 135006516 1014888 0.007517326052618082 0.09978827204373908 chr12 133851895 1003209 0.007494918170564563 0.09150455957928222 chr13 115169878 689205 0.00598424702681373 0.08137641345149274 chr14 107349540 679558 0.00633032987379359 0.08460614569058539 chr15 102531392 650673 0.00634608569441835 0.08391143462495541 chr16 90354753 678359 0.007507729006796134 0.09202712570501102 chr17 81195210 648366 0.007985274008158856 0.09592937291485754 chr18 78077248 578423 0.007408342568631517 0.11661089570251695 chr19 59128983 493024 0.008338110601361096 0.10716411879850314 chr20 63025520 509462 0.008083423984443127 0.09619917890590778 chr21 48129895 295456 0.006138721058917747 0.08681007860671228 chr22 51304566 278606 0.005430432839057638 0.07799812078682511 chrMT 16571 3345 0.20185866875867478 0.4578539535415794 chrX 155270560 1124574 0.0072426736916515275 0.09204721059409843 chrY 59373566 96237 0.0016208728308486642 0.05362849134463561