BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013198.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,721,040 number of mapped reads = 1,385,227 (80.49%) number of supplementary alignments = 9,770 (0.57%) number of secondary alignments = 0 number of mapped bases = 95,503,297 bp number of sequenced bases = 95,472,399 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,661 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.375 >>>>>>> ACTG content number of A's = 30,348,507 bp (31.79%) number of C's = 16,408,664 bp (17.19%) number of T's = 28,341,782 bp (29.69%) number of G's = 20,334,016 bp (21.3%) number of N's = 39,430 bp (0.04%) GC percentage = 38.49% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 1,027,929 number of insertions = 5,777 mapped reads with insertion percentage = 0.41% number of deletions = 18,538 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2111X There is a 2.93% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 7391434 0.029654626216558153 0.3248981808423496 chr2 243199373 7923264 0.032579294519809475 0.20699725868928617 chr3 198022430 7099624 0.03585262538188225 0.19435182992291603 chr4 191154276 6540987 0.03421836611177874 0.19210456142022944 chr5 180915260 5709052 0.03155649777691501 0.18286017572456578 chr6 171115067 5831380 0.03407870564665121 0.20418032920740042 chr7 159138663 5433113 0.03414074805944549 0.24443728497646905 chr8 146364022 4890288 0.03341181755718629 0.23897630142541995 chr9 141213431 4131577 0.029257677338071334 0.1926409816320153 chr10 135534747 4426055 0.032656238329791545 0.20701765374821743 chr11 135006516 4348463 0.03220928240233975 0.19905305465565526 chr12 133851895 4351167 0.032507324606797686 0.18579287315907206 chr13 115169878 3612489 0.031366613065266946 0.18215368142226837 chr14 107349540 3055928 0.028467080529641767 0.1759457356199074 chr15 102531392 2489137 0.024276828310299346 0.16287122438761178 chr16 90354753 2112242 0.02337720960844196 0.1624768876730398 chr17 81195210 2006789 0.024715608223687086 0.16810827207929224 chr18 78077248 2871487 0.03677751295742391 0.2805793556919797 chr19 59128983 1202620 0.020338925836082787 0.20874698512594267 chr20 63025520 1755802 0.027858588076702898 0.17387248683213924 chr21 48129895 1341739 0.02787745537363005 0.1772083512877002 chr22 51304566 793839 0.015473067250973334 0.12865480139604257 chrMT 16571 5091 0.30722346267575884 0.6971118704779314 chrX 155270560 5997934 0.038628919738551856 0.20870950444139724 chrY 59373566 181796 0.0030619013181724677 0.06785730128397681