BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717018.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 = 1,085,930 number of mapped reads = 1,026,225 (94.5%) number of supplementary alignments = 23,747 (2.19%) number of secondary alignments = 0 number of mapped bases = 79,671,033 bp number of sequenced bases = 79,638,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,118 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6646 >>>>>>> ACTG content number of A's = 20,042,858 bp (25.17%) number of C's = 16,778,557 bp (21.07%) number of T's = 23,405,230 bp (29.39%) number of G's = 19,408,496 bp (24.37%) number of N's = 3,044 bp (0%) GC percentage = 45.44% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 522,193 number of insertions = 7,182 mapped reads with insertion percentage = 0.69% number of deletions = 15,675 mapped reads with deletion percentage = 1.5% homopolymer indels = 38.55% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2234X There is a 2.29% of reference with a coverageData >= 1X There is a 0.21% 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 6555176 0.02629953728380079 0.28655012284485815 chr2 243199373 6698909 0.027544927099791495 0.2559770776309434 chr3 198022430 5138140 0.02594726264090386 0.1756736636254785 chr4 191154276 4986234 0.026084867701311583 0.23987649209811623 chr5 180915260 4680222 0.025869691699859924 0.17628267788245988 chr6 171115067 4485877 0.02621555821264997 0.18115473483798394 chr7 159138663 4288311 0.02694700909985652 0.2619124053159621 chr8 146364022 4063858 0.027765416285157836 0.23506459612716565 chr9 141213431 3242339 0.022960556775934435 0.19861070655850852 chr10 135534747 3891461 0.028711906622734908 0.30776447439919175 chr11 135006516 3618236 0.02680045457954044 0.23074076855051295 chr12 133851895 3599534 0.026891916621725825 0.18119590116100387 chr13 115169878 2400311 0.02084148252722817 0.15773002858185345 chr14 107349540 2422396 0.022565499582019633 0.1769598504933771 chr15 102531392 2310482 0.0225343863467688 0.16404597714464153 chr16 90354753 2534226 0.028047511789446207 0.19828692963064656 chr17 81195210 2284030 0.02813010767507098 0.20315946834121135 chr18 78077248 2148274 0.027514724904238428 0.30350500934234237 chr19 59128983 1740252 0.029431454960082773 0.23619886359090012 chr20 63025520 1795533 0.02848898351017175 0.1926846135225124 chr21 48129895 1060329 0.02203056956596311 0.21108227245488648 chr22 51304566 1102379 0.021486956930889933 0.16374681228132068 chrMT 16571 19309 1.165228411079597 1.3470677466805583 chrX 155270560 4317922 0.027809019301534045 0.19512909187568142 chrY 59373566 287293 0.004838735810478353 0.20631712011801945