BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173962.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,453,602 number of mapped reads = 1,415,088 (97.35%) number of supplementary alignments = 144,372 (9.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 707,735 number of mapped paired reads (second in pair) = 707,353 number of mapped paired reads (both in pair) = 1,390,662 number of mapped paired reads (singletons) = 24,426 number of mapped bases = 167,534,771 bp number of sequenced bases = 167,437,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,060,550 duplication rate = 61.66% >>>>>>> Insert size mean insert size = 1,086,897.2226 std insert size = 9,441,832.8991 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.8773 >>>>>>> ACTG content number of A's = 50,732,819 bp (30.3%) number of C's = 32,497,584 bp (19.41%) number of T's = 50,495,689 bp (30.16%) number of G's = 33,709,792 bp (20.13%) number of N's = 1,969 bp (0%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 1,793,724 number of insertions = 19,609 mapped reads with insertion percentage = 1.33% number of deletions = 39,814 mapped reads with deletion percentage = 2.75% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.9633X There is a 1.27% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 13584480 0.05450128848425216 0.8246200714825309 chr2 243199373 14750516 0.060651949131464246 2.3895541807946685 chr3 198022430 11244364 0.056783284600638424 0.6640341633536553 chr4 191154276 11848050 0.06198161112545555 0.8047716866664595 chr5 180915260 10654973 0.05889482733518444 0.6772724124700024 chr6 171115067 9920945 0.057978208312889246 0.7067363175770803 chr7 159138663 9201004 0.05781752734720412 0.7358191309926319 chr8 146364022 8864553 0.06056510936820252 0.8156895784077396 chr9 141213431 7365352 0.052157588324583656 0.7728041668213061 chr10 135534747 8268272 0.06100481376926907 0.9499324181669366 chr11 135006516 7589984 0.05621939018113763 0.6582569298884328 chr12 133851895 7539240 0.056325239175732254 0.6646627020600901 chr13 115169878 5422806 0.04708528040639237 0.6131410858435772 chr14 107349540 5309372 0.04945873079661077 0.6241395190552406 chr15 102531392 4846945 0.047272790366486 0.600001632668546 chr16 90354753 5118605 0.05665009122431003 0.7249950502823058 chr17 81195210 4421749 0.05445824944599564 0.6574809859784085 chr18 78077248 4692736 0.060103757755396295 0.9102777835096012 chr19 59128983 2834496 0.04793750638329092 0.6644385552327392 chr20 63025520 3483982 0.05527890924184362 0.6770696926598497 chr21 48129895 2322350 0.04825171548784804 0.7215065596150605 chr22 51304566 1950994 0.0380276874381902 0.541891140853759 chrMT 16571 282538 17.050147848651257 16.819671471670798 chrX 155270560 4694140 0.030232002769874727 0.4808713080498789 chrY 59373566 1322325 0.02227127472855513 0.5354521941771324