BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716125.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 = 2,209,447 number of mapped reads = 2,068,685 (93.63%) number of supplementary alignments = 40,652 (1.84%) number of secondary alignments = 0 number of mapped bases = 164,007,389 bp number of sequenced bases = 163,929,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,349 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4597 >>>>>>> ACTG content number of A's = 41,877,003 bp (25.55%) number of C's = 32,863,804 bp (20.05%) number of T's = 49,493,167 bp (30.19%) number of G's = 39,683,810 bp (24.21%) number of N's = 11,418 bp (0.01%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,055,352 number of insertions = 13,037 mapped reads with insertion percentage = 0.62% number of deletions = 40,411 mapped reads with deletion percentage = 1.92% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.4741X There is a 4.43% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 16137849 0.0647454715870096 0.9984257009038039 chr2 243199373 13493067 0.05548150405798949 0.4955739391849886 chr3 198022430 10517995 0.05311516983202357 0.26250553288689216 chr4 191154276 10255883 0.053652385992139666 0.3578562212577039 chr5 180915260 9380263 0.051848931925366604 0.26270459651566336 chr6 171115067 8779845 0.05130959624963943 0.2842210042980827 chr7 159138663 8586516 0.053956190394787974 0.5584912206473382 chr8 146364022 8097653 0.055325433732614976 0.5219300959835322 chr9 141213431 6702522 0.04746377134622556 0.4052850360144498 chr10 135534747 7696540 0.05678647114750581 0.4723091654861112 chr11 135006516 9129624 0.06762358047962663 0.5263703443654203 chr12 133851895 7015633 0.05241340064703604 0.2622826889955264 chr13 115169878 5703463 0.04952217627598772 0.2555316173202237 chr14 107349540 4636271 0.043188550225739204 0.2599548552622502 chr15 102531392 4613705 0.04499797486412747 0.24253630397695541 chr16 90354753 3657885 0.04048359249014825 0.2625226101630749 chr17 81195210 5210014 0.0641665191825971 0.356125822921687 chr18 78077248 4184188 0.0535903622012907 0.6649977643927925 chr19 59128983 3277410 0.05542814764799861 0.6793481508850222 chr20 63025520 3349707 0.05314842305148772 0.28185909946761095 chr21 48129895 2136513 0.04439056017055512 0.2965204216922655 chr22 51304566 1932566 0.0376684991351452 0.22520471184440338 chrMT 16571 91593 5.52730674069157 3.6188989897055435 chrX 155270560 8908365 0.057373174927687516 0.32814192422665495 chrY 59373566 512319 0.008628738923985128 0.2913339310533669