BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524633.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 = 1,714,085 number of mapped reads = 1,567,427 (91.44%) number of supplementary alignments = 5,525 (0.32%) number of secondary alignments = 0 number of mapped bases = 90,054,691 bp number of sequenced bases = 90,030,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,315 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6193 >>>>>>> ACTG content number of A's = 24,086,670 bp (26.75%) number of C's = 18,372,276 bp (20.41%) number of T's = 27,314,568 bp (30.34%) number of G's = 20,254,545 bp (22.5%) number of N's = 2,655 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 431,021 number of insertions = 6,767 mapped reads with insertion percentage = 0.43% number of deletions = 14,289 mapped reads with deletion percentage = 0.91% homopolymer indels = 40.95% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.2688X There is a 2.62% 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 6376825 0.025583988414616628 0.4255823502714129 chr2 243199373 7470099 0.030715946788234524 0.30624302444718854 chr3 198022430 5530147 0.027926871718521987 0.1786253490370057 chr4 191154276 5588626 0.02923620709379266 0.20322071667438765 chr5 180915260 5021691 0.027757144422200758 0.180779639681399 chr6 171115067 4033425 0.023571419342050107 0.18070897137476266 chr7 159138663 5819948 0.03657155269678243 0.36989826646287277 chr8 146364022 3892635 0.02659557278359022 0.24591953082563398 chr9 141213431 4216431 0.029858569189498696 0.2894288948503592 chr10 135534747 3490197 0.025751307891547545 0.2634370693569688 chr11 135006516 3432496 0.025424669132266178 0.22288008880591859 chr12 133851895 6721821 0.050218347674495005 0.27066511702887164 chr13 115169878 3557381 0.030888119895377503 0.18869968766686093 chr14 107349540 3295024 0.030694346710754418 0.20575566399865192 chr15 102531392 2355257 0.022971081871199017 0.16358351364979767 chr16 90354753 2592286 0.02869009004982837 0.19989573151615886 chr17 81195210 2691700 0.033150970358965755 0.20333274825857806 chr18 78077248 2784001 0.03565700727566627 0.5349212034257265 chr19 59128983 1528892 0.025856896608554895 0.33691084845766006 chr20 63025520 2714072 0.0430630639778934 0.2312912834097503 chr21 48129895 1163067 0.024165168031220513 0.19326633326216877 chr22 51304566 880515 0.017162507524184106 0.1395720056125864 chrMT 16571 6109 0.3686560859332569 0.6479127065794749 chrX 155270560 4626264 0.029794856153027335 0.21555052817585507 chrY 59373566 265782 0.004476436534062987 0.11213080715566912