BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716577.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 = 1,571,726 number of mapped reads = 1,446,732 (92.05%) number of supplementary alignments = 8,153 (0.52%) number of secondary alignments = 0 number of mapped bases = 84,677,828 bp number of sequenced bases = 84,652,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,499 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7377 >>>>>>> ACTG content number of A's = 20,351,372 bp (24.04%) number of C's = 16,328,654 bp (19.29%) number of T's = 26,649,266 bp (31.48%) number of G's = 21,322,423 bp (25.19%) number of N's = 962 bp (0%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 432,136 number of insertions = 4,858 mapped reads with insertion percentage = 0.33% number of deletions = 15,800 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.271X There is a 2.45% of reference with a coverageData >= 1X There is a 0.2% 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 7082689 0.02841593321446529 0.38190942900193975 chr2 243199373 9237652 0.03798386437451876 0.33357874161621953 chr3 198022430 6177210 0.031194496502239672 0.20297822061379275 chr4 191154276 4623435 0.02418692951446192 0.18710307903341958 chr5 180915260 4254133 0.023514506183723805 0.16658795496323933 chr6 171115067 4722580 0.02759885545321383 0.1942205409109173 chr7 159138663 5238327 0.03291674632204243 0.577295207292492 chr8 146364022 5913109 0.04040001715722188 0.28559992272872403 chr9 141213431 3602880 0.02551372043357547 0.19918305989896576 chr10 135534747 4021815 0.02967368212964606 0.3642367023072594 chr11 135006516 2584970 0.019147001763974117 0.18605314319357114 chr12 133851895 3965268 0.02962429482227353 0.20994612842458824 chr13 115169878 2178741 0.01891762879179224 0.14949949573951565 chr14 107349540 2135928 0.019896945995297233 0.15698841961935153 chr15 102531392 2017887 0.01968067496830629 0.15312566699403662 chr16 90354753 2318761 0.025662855832277023 0.18337539427478766 chr17 81195210 3654770 0.045012138031295196 0.23984641321346944 chr18 78077248 1916788 0.024549891922420217 0.28225499031922574 chr19 59128983 1729474 0.029249175484719565 0.32745423934020174 chr20 63025520 1955747 0.03103103314339969 0.2011332793352221 chr21 48129895 879346 0.01827026632823529 0.15847556615432384 chr22 51304566 1301554 0.025369164997906812 0.1742890621987676 chrMT 16571 38840 2.343853720354837 2.410626817503641 chrX 155270560 2930544 0.018873790369533027 0.16802851931957385 chrY 59373566 195380 0.0032906900016751563 0.09545951217982232