BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716220.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 = 3,009,525 number of mapped reads = 2,772,166 (92.11%) number of supplementary alignments = 19,589 (0.65%) number of secondary alignments = 0 number of mapped bases = 161,819,553 bp number of sequenced bases = 161,774,382 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,845 duplication rate = 5.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8704 >>>>>>> ACTG content number of A's = 38,748,856 bp (23.95%) number of C's = 34,190,402 bp (21.13%) number of T's = 50,425,933 bp (31.17%) number of G's = 38,407,073 bp (23.74%) number of N's = 2,118 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 802,700 number of insertions = 11,666 mapped reads with insertion percentage = 0.42% number of deletions = 28,695 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.44% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.3982X There is a 4.15% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12917064 0.05182359806437554 0.6082550203366506 chr2 243199373 13525528 0.05561497890868329 0.5547313559771773 chr3 198022430 11212056 0.05662013136592658 0.29050281374295833 chr4 191154276 10159306 0.05314715533750341 0.3325511932012848 chr5 180915260 9641022 0.05329026418224753 0.2826087420293319 chr6 171115067 9304751 0.054377157798734345 0.3179931562915811 chr7 159138663 8887776 0.05584925644373423 0.520429823018985 chr8 146364022 8314751 0.05680870808537907 0.4369453673534633 chr9 141213431 6698074 0.04743227292593719 0.3328402095861371 chr10 135534747 7628223 0.056282415903281244 0.42892091407409594 chr11 135006516 7180306 0.05318488479474576 0.36409620653114094 chr12 133851895 7246849 0.054140802414489535 0.28915890711301123 chr13 115169878 4876977 0.0423459422263172 0.2516488296581137 chr14 107349540 5204281 0.04847976991797077 0.28434982746600745 chr15 102531392 4690080 0.045742868681622896 0.2654577829814335 chr16 90354753 4786278 0.05297206667146774 0.30111859500318355 chr17 81195210 4629233 0.05701362186266899 0.3173903488214287 chr18 78077248 4328166 0.05543440772912488 0.5985622232809171 chr19 59128983 3412391 0.05771097060810263 0.47898361853371996 chr20 63025520 3579206 0.05678978927900952 0.3022473208070197 chr21 48129895 2074480 0.04310169386407346 0.29296329928125575 chr22 51304566 2157783 0.04205830334867271 0.2527245992791637 chrMT 16571 23089 1.3933377587351397 1.5569957556912966 chrX 155270560 8838112 0.056920719549153426 0.31924707276327546 chrY 59373566 503771 0.008484769131097835 0.22588481135349245