BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004074.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 = 2,459,549 number of mapped reads = 2,254,146 (91.65%) number of supplementary alignments = 17,641 (0.72%) number of secondary alignments = 0 number of mapped bases = 152,434,013 bp number of sequenced bases = 152,369,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,528 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9354 >>>>>>> ACTG content number of A's = 43,686,051 bp (28.67%) number of C's = 28,308,406 bp (18.58%) number of T's = 48,183,458 bp (31.62%) number of G's = 32,164,509 bp (21.11%) number of N's = 27,101 bp (0.02%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,301,169 number of insertions = 10,886 mapped reads with insertion percentage = 0.48% number of deletions = 36,841 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.3893X There is a 3.94% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 11576177 0.04644392440651131 0.6230194147372248 chr2 243199373 11913426 0.0489862529374202 0.4073621451011941 chr3 198022430 10751689 0.05429530886980834 0.2787564020541303 chr4 191154276 10761216 0.05629597320647957 0.30238533157620323 chr5 180915260 9502900 0.052526801774488235 0.27570714856394524 chr6 171115067 9950192 0.058149128387390926 0.3143072358331121 chr7 159138663 8609227 0.05409890241443087 0.5451656391048143 chr8 146364022 11439009 0.07815451395562224 0.6574016584804241 chr9 141213431 5673969 0.04018009448407213 0.34101235591659945 chr10 135534747 6758093 0.04986243859665005 0.362596782623577 chr11 135006516 5703102 0.042243161063426 0.3079806065229759 chr12 133851895 6828422 0.0510147577664104 0.27759481796969815 chr13 115169878 4976590 0.043210864563041386 0.2549708576668493 chr14 107349540 3678981 0.03427104578184499 0.2423288764024461 chr15 102531392 5319477 0.05188144719619139 0.2729800889096801 chr16 90354753 3591374 0.039747482902199954 0.26361152368706314 chr17 81195210 3160711 0.03892730864296059 0.2507768312978508 chr18 78077248 4109882 0.0526386636988025 0.6075935265334553 chr19 59128983 1936018 0.03274228477766986 0.4451821103247807 chr20 63025520 3079875 0.04886710970413255 0.272313960466667 chr21 48129895 1744856 0.036253060597784395 0.24533869106423056 chr22 51304566 1099665 0.02143405715584847 0.17111230154266524 chrMT 16571 30361 1.8321766942248507 1.9292949436049416 chrX 155270560 9857847 0.06348819119348832 0.32583944021351496 chrY 59373566 380954 0.006416222330321207 0.13638454448484813