BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716866.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 = 2,680,122 number of mapped reads = 2,322,656 (86.66%) number of supplementary alignments = 8,870 (0.33%) number of secondary alignments = 0 number of mapped bases = 133,164,388 bp number of sequenced bases = 133,122,520 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,779 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5749 >>>>>>> ACTG content number of A's = 32,701,209 bp (24.56%) number of C's = 26,721,612 bp (20.07%) number of T's = 40,917,959 bp (30.74%) number of G's = 32,779,698 bp (24.62%) number of N's = 2,042 bp (0%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 680,326 number of insertions = 8,359 mapped reads with insertion percentage = 0.36% number of deletions = 25,512 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.043X std coverageData = 0.3309X There is a 3.72% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10706853 0.04295617381831919 0.4719910523723458 chr2 243199373 11241290 0.046222528706930506 0.4899301877775932 chr3 198022430 8751142 0.04419268059683946 0.24122220259463464 chr4 191154276 8518050 0.04456112715992814 0.28653007227464244 chr5 180915260 7902650 0.04368150038863499 0.2355043135271747 chr6 171115067 7508739 0.043881226426425675 0.2751463543269397 chr7 159138663 7358584 0.04624007680647663 0.4292705805963316 chr8 146364022 6654725 0.04546694542187424 0.32029820161212064 chr9 141213431 5528612 0.039150751885633314 0.27485610287642 chr10 135534747 6420010 0.04736800076809824 0.3968794025368108 chr11 135006516 5981678 0.04430658739464101 0.2986475414199829 chr12 133851895 6048822 0.04519040989296416 0.2436105720258575 chr13 115169878 4087562 0.035491589215714894 0.21324899407269676 chr14 107349540 4048716 0.03771526175147094 0.22875719825217491 chr15 102531392 3925336 0.03828423591479183 0.22665687302366003 chr16 90354753 4064925 0.04498850215439137 0.2646303307306115 chr17 81195210 3843741 0.04733950438701987 0.2680468234266026 chr18 78077248 3449399 0.044179310725705905 0.47059296827843916 chr19 59128983 3015812 0.05100395520078538 0.40682639303376983 chr20 63025520 2874209 0.04560389188379564 0.25080357312934115 chr21 48129895 1733420 0.036015453596979594 0.2483735173910389 chr22 51304566 1706531 0.033262750921623625 0.20857841006460023 chrMT 16571 8953 0.540281214169332 0.9737345653719143 chrX 155270560 7363945 0.047426537265016624 0.2727679642461878 chrY 59373566 420684 0.0070853753335280555 0.19395172172141067