BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068082.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 = 2,522,674 number of mapped reads = 2,157,889 (85.54%) number of supplementary alignments = 22,096 (0.88%) number of secondary alignments = 0 number of mapped bases = 139,192,146 bp number of sequenced bases = 139,135,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 269,224 duplication rate = 9.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8507 >>>>>>> ACTG content number of A's = 36,579,915 bp (26.29%) number of C's = 25,789,286 bp (18.54%) number of T's = 44,003,486 bp (31.63%) number of G's = 32,759,688 bp (23.55%) number of N's = 2,667 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,130,833 number of insertions = 10,336 mapped reads with insertion percentage = 0.48% number of deletions = 35,951 mapped reads with deletion percentage = 1.65% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.4525X There is a 2.98% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 11783492 0.04727567760001689 0.7085691306260833 chr2 243199373 8639378 0.035523849808609495 0.6837845896925144 chr3 198022430 10286684 0.05194706478452971 0.31961918781722104 chr4 191154276 10028352 0.05246208565065005 0.3498608601952801 chr5 180915260 9169748 0.05068532085132012 0.3178082673499802 chr6 171115067 8393607 0.04905241336813432 0.345422283057498 chr7 159138663 9443745 0.05934287006043277 0.6759466745271524 chr8 146364022 8238995 0.056291121871466475 0.5251482810192502 chr9 141213431 5621916 0.03981148223783331 0.3743435354830366 chr10 135534747 5560502 0.04102639450826584 0.3699210330240297 chr11 135006516 4876541 0.036120782496157446 0.3955430844544675 chr12 133851895 4165736 0.031121980006334614 0.2514557775650304 chr13 115169878 4292476 0.03727082180290232 0.27333213604187745 chr14 107349540 5366063 0.04998682807583526 0.32039301813105153 chr15 102531392 4542742 0.04430586488087473 0.3045089078430321 chr16 90354753 3653926 0.040439776311490774 0.2938798840278558 chr17 81195210 1739354 0.021421879443380958 0.24142843074810386 chr18 78077248 4310775 0.05521166678415715 0.6410860898002461 chr19 59128983 2890285 0.048881019989807706 0.5415544947875319 chr20 63025520 1552154 0.024627389032252332 0.23011379345704103 chr21 48129895 1419543 0.02949399744171476 0.25621507936729526 chr22 51304566 1210809 0.023600414045018916 0.21220865491787444 chrMT 16571 26511 1.5998430993905015 2.125754331981383 chrX 155270560 11549473 0.07438289009841917 0.4308147786838148 chrY 59373566 429339 0.007231147275203244 0.20191383922765913