BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716554.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 = 3,075,750 number of mapped reads = 2,722,323 (88.51%) number of supplementary alignments = 10,205 (0.33%) number of secondary alignments = 0 number of mapped bases = 154,924,064 bp number of sequenced bases = 154,879,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,069 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3475 >>>>>>> ACTG content number of A's = 39,052,528 bp (25.21%) number of C's = 31,192,654 bp (20.14%) number of T's = 47,769,262 bp (30.84%) number of G's = 36,863,417 bp (23.8%) number of N's = 1,139 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 801,710 number of insertions = 12,881 mapped reads with insertion percentage = 0.47% number of deletions = 28,680 mapped reads with deletion percentage = 1.05% homopolymer indels = 38.83% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.372X There is a 4.3% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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 13162669 0.05280897173772738 0.4848145230982974 chr2 243199373 12338254 0.050733083098861445 0.5793019023147425 chr3 198022430 9061578 0.04576036159136114 0.24993742466558788 chr4 191154276 9584710 0.05014122728805711 0.274264232600847 chr5 180915260 8954860 0.049497538239726156 0.25174235841855025 chr6 171115067 8415894 0.0491826590583049 0.3221116300804996 chr7 159138663 8756187 0.055022373789831325 0.5750112092314638 chr8 146364022 8220464 0.05616451288828343 0.3572805783140498 chr9 141213431 5155055 0.036505415692364276 0.27206110877653705 chr10 135534747 6261729 0.04620017477879676 0.4614099142564394 chr11 135006516 5495379 0.040704546438336354 0.3057181977702807 chr12 133851895 7811784 0.05836140011316239 0.2772659140700295 chr13 115169878 4780953 0.041512182551760625 0.23298060021061967 chr14 107349540 5254971 0.048951965700085906 0.27451594646295174 chr15 102531392 5736919 0.05595280516624606 0.2821800577245911 chr16 90354753 5388463 0.05963674096923269 0.3046804804564031 chr17 81195210 6860984 0.08449986150660858 0.36205232700111156 chr18 78077248 2890017 0.037014842019021985 0.4678415784034291 chr19 59128983 3895761 0.06588581102434994 0.4619420348207054 chr20 63025520 4536576 0.0719799852504192 0.32572408311335416 chr21 48129895 1956747 0.04065554267259465 0.2461444721951037 chr22 51304566 1394061 0.027172259872542338 0.19048463509373986 chrMT 16571 3109 0.18761692112727052 0.5105665799755933 chrX 155270560 8556806 0.05510900456596537 0.2970029637791967 chrY 59373566 450134 0.007581387313000536 0.18300233201397237