BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716400.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 = 2,261,292 number of mapped reads = 2,062,209 (91.2%) number of supplementary alignments = 34,576 (1.53%) number of secondary alignments = 0 number of mapped bases = 161,433,710 bp number of sequenced bases = 161,363,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,627 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8146 >>>>>>> ACTG content number of A's = 39,366,399 bp (24.4%) number of C's = 31,252,872 bp (19.37%) number of T's = 52,164,018 bp (32.33%) number of G's = 38,570,907 bp (23.9%) number of N's = 8,965 bp (0.01%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,354,328 number of insertions = 14,849 mapped reads with insertion percentage = 0.71% number of deletions = 40,635 mapped reads with deletion percentage = 1.94% homopolymer indels = 44.47% >>>>>>> Coverage mean coverageData = 0.0521X std coverageData = 0.6094X There is a 4.39% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 12823769 0.05144929608821316 1.0214013222867053 chr2 243199373 13953476 0.057374638050567674 0.8920361253922765 chr3 198022430 10725426 0.054162682479959465 0.2710255239200087 chr4 191154276 10438464 0.054607535956977496 0.2953914206185983 chr5 180915260 9765499 0.053978304538821104 0.27774303437701886 chr6 171115067 9360863 0.05470507749034163 0.37300704377452115 chr7 159138663 9014853 0.05664778646531673 0.7979423828420348 chr8 146364022 8094924 0.05530678844012636 0.8259549116400678 chr9 141213431 6834128 0.04839573652169105 0.6864428624605571 chr10 135534747 7726771 0.05700952096070242 0.5541391161692705 chr11 135006516 7257268 0.05375494616867233 0.5857437887416442 chr12 133851895 7354835 0.05494755976372243 0.2834852904117619 chr13 115169878 5095260 0.04424125551300836 0.23819742807620362 chr14 107349540 4860622 0.04527846137021174 0.3923257149798181 chr15 102531392 4551601 0.04439226768714893 0.24845440410629913 chr16 90354753 4592510 0.050827541966718674 0.3267802445104292 chr17 81195210 4293928 0.05288400633485645 0.31131441162701545 chr18 78077248 4475448 0.05732077032223267 1.3112906156013402 chr19 59128983 3303537 0.055870012173218 0.7707031789054606 chr20 63025520 3227442 0.0512084945907626 0.2885887558167706 chr21 48129895 2088453 0.043392012386480376 0.2673045411936103 chr22 51304566 1739202 0.03389955584070237 0.21022488186778354 chrMT 16571 14187 0.8561342103675095 1.1156480049285877 chrX 155270560 9409819 0.060602724689084654 0.44791100443937276 chrY 59373566 431425 0.00726628075531121 0.1898191991124492