BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716702.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 = 1,574,924 number of mapped reads = 1,448,037 (91.94%) number of supplementary alignments = 22,385 (1.42%) number of secondary alignments = 0 number of mapped bases = 114,597,427 bp number of sequenced bases = 114,548,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,969 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7639 >>>>>>> ACTG content number of A's = 27,327,681 bp (23.86%) number of C's = 21,930,973 bp (19.15%) number of T's = 35,811,278 bp (31.26%) number of G's = 29,471,495 bp (25.73%) number of N's = 6,838 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 955,859 number of insertions = 10,619 mapped reads with insertion percentage = 0.72% number of deletions = 27,999 mapped reads with deletion percentage = 1.9% homopolymer indels = 43.76% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.5002X There is a 3.17% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10319864 0.041403563845082654 0.7073859972953722 chr2 243199373 8985030 0.03694511992018992 0.9288538151926656 chr3 198022430 8621141 0.0435361842595306 0.2475821912679048 chr4 191154276 4662376 0.024390644549327267 0.19325110892105637 chr5 180915260 7124210 0.039378712442499325 0.22923276273671467 chr6 171115067 8355101 0.048827383505626654 0.31312068669044 chr7 159138663 5278518 0.03316929965661456 0.6631518664236914 chr8 146364022 8067445 0.055119044214294685 0.6984747968678057 chr9 141213431 5107112 0.03616590832638292 0.49338920157510247 chr10 135534747 5679082 0.04190129930297505 0.4336501007810095 chr11 135006516 4681257 0.03467430416469676 0.3357417268774304 chr12 133851895 4377626 0.03270499831175345 0.21142431386945296 chr13 115169878 3990786 0.0346513000560789 0.20862000078290502 chr14 107349540 2778112 0.0258791234689967 0.23443957482233446 chr15 102531392 2300552 0.022437537959106222 0.1744171969231874 chr16 90354753 3119868 0.03452909665969647 0.25512109020717444 chr17 81195210 3747407 0.046153055087855555 0.29530968538573243 chr18 78077248 3681910 0.047157271731708576 1.1305277318201143 chr19 59128983 2403517 0.04064871198613377 0.5789638987393431 chr20 63025520 2093503 0.0332167509288301 0.2656803090070508 chr21 48129895 2417956 0.050238131622767926 0.26515793409228633 chr22 51304566 1768330 0.03446730257887768 0.21099373577866168 chrMT 16571 4204 0.25369621628145556 0.6818181978802265 chrX 155270560 4744672 0.030557447593413715 0.2985292065836172 chrY 59373566 287848 0.004848083404658565 0.14749949725151074