BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716259.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 = 519,831 number of mapped reads = 440,170 (84.68%) number of supplementary alignments = 1,878 (0.36%) number of secondary alignments = 0 number of mapped bases = 25,319,099 bp number of sequenced bases = 25,311,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,891 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4396 >>>>>>> ACTG content number of A's = 6,528,436 bp (25.79%) number of C's = 4,473,362 bp (17.67%) number of T's = 8,008,104 bp (31.64%) number of G's = 6,301,334 bp (24.89%) number of N's = 715 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 128,624 number of insertions = 1,702 mapped reads with insertion percentage = 0.39% number of deletions = 4,466 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0082X std coverageData = 0.1101X There is a 0.78% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 3066228 0.01230178680276989 0.16868416518247276 chr2 243199373 2195108 0.00902596077005511 0.1343936185295207 chr3 198022430 2339087 0.011812232583955262 0.11419008096433457 chr4 191154276 1222947 0.006397696277534487 0.08462597225701429 chr5 180915260 1148977 0.006350912576418374 0.0826966819660055 chr6 171115067 1691840 0.009887148044070251 0.10951581974598532 chr7 159138663 1055332 0.006631524860806453 0.10298658884105175 chr8 146364022 1843921 0.012598184818944098 0.12115964150866117 chr9 141213431 1060262 0.0075082234918575136 0.1040210443680592 chr10 135534747 1314662 0.009699815206797118 0.1380490535466768 chr11 135006516 844684 0.006256616532493884 0.08968369181833825 chr12 133851895 1145019 0.008554372726661808 0.096504808735981 chr13 115169878 599073 0.0052016465624805126 0.07431467293906563 chr14 107349540 567038 0.005282165158788757 0.07747903398779031 chr15 102531392 762857 0.0074402286472420075 0.08875056610107195 chr16 90354753 544338 0.006024453411985975 0.08827808025999298 chr17 81195210 682675 0.008407823564961529 0.0953923230061625 chr18 78077248 500391 0.006408922097254247 0.1324085396864201 chr19 59128983 553843 0.009366692472962033 0.12956794386011333 chr20 63025520 424655 0.00673782620119596 0.08503031491817138 chr21 48129895 241454 0.005016715702371675 0.07697843175987922 chr22 51304566 299006 0.005828058266782727 0.07863632784379494 chrMT 16571 32864 1.9832237040613119 1.7730467885577414 chrX 155270560 1121474 0.007222708541786672 0.09336682009100923 chrY 59373566 61364 0.0010335239086026937 0.038178031165511404