BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013355.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 = 2,320,943 number of mapped reads = 2,050,985 (88.37%) number of supplementary alignments = 17,027 (0.73%) number of secondary alignments = 0 number of mapped bases = 138,751,858 bp number of sequenced bases = 138,694,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,694 duplication rate = 4.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.14 >>>>>>> ACTG content number of A's = 38,969,553 bp (28.1%) number of C's = 25,539,949 bp (18.41%) number of T's = 44,280,765 bp (31.93%) number of G's = 29,874,702 bp (21.54%) number of N's = 29,229 bp (0.02%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,110,331 number of insertions = 10,064 mapped reads with insertion percentage = 0.49% number of deletions = 33,173 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.5354X There is a 3.56% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% 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 15013225 0.060233450732305294 1.0005864261399369 chr2 243199373 14347928 0.05899656657420741 0.608586841695233 chr3 198022430 6478593 0.03271646045349509 0.21670418500004657 chr4 191154276 4921813 0.02574785719153884 0.21838373504984201 chr5 180915260 4238680 0.0234290905034766 0.182212064227068 chr6 171115067 5520385 0.032261244417477276 0.22351552003254668 chr7 159138663 14120503 0.08873081332849957 1.330076436886533 chr8 146364022 10175795 0.06952388203707602 0.5239643467702754 chr9 141213431 5376059 0.03807045096156611 0.38739026094734547 chr10 135534747 5084821 0.037516733624035174 0.4659574693213007 chr11 135006516 8164723 0.060476510630049884 0.36320774836221764 chr12 133851895 7554755 0.056441150870519985 0.29362527138424405 chr13 115169878 455335 0.003953594532764895 0.0778238050205137 chr14 107349540 4716903 0.04393966662549276 0.25479708996739814 chr15 102531392 1187149 0.011578395424495944 0.1315223224329612 chr16 90354753 4519543 0.05001998068657218 0.278067664695396 chr17 81195210 5617624 0.06918664290664436 0.3945586495029754 chr18 78077248 6610815 0.0846701845843747 0.5790463596195562 chr19 59128983 1981746 0.033515644941838424 0.7590979019591625 chr20 63025520 3237022 0.051360496509985164 0.2738005671640673 chr21 48129895 1368980 0.02844344455769122 0.2146638287770708 chr22 51304566 1404773 0.027381052204983082 0.19374104278643056 chrMT 16571 30797 1.8584877195099874 1.735690873033005 chrX 155270560 6361136 0.04096807533894384 0.284614392055558 chrY 59373566 262755 0.0044254542501287525 0.12147600414452195