BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716505.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 = 547,475 number of mapped reads = 415,001 (75.8%) number of supplementary alignments = 773 (0.14%) number of secondary alignments = 0 number of mapped bases = 23,868,672 bp number of sequenced bases = 23,860,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,373 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9678 >>>>>>> ACTG content number of A's = 5,586,557 bp (23.41%) number of C's = 4,180,690 bp (17.52%) number of T's = 8,000,424 bp (33.53%) number of G's = 6,093,093 bp (25.54%) number of N's = 227 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 119,146 number of insertions = 1,532 mapped reads with insertion percentage = 0.37% number of deletions = 4,788 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0077X std coverageData = 0.1041X There is a 0.74% 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 2849576 0.011432573321452226 0.13694905328948329 chr2 243199373 2457838 0.010106267831537542 0.1385273531764138 chr3 198022430 1532522 0.007739133390091213 0.0919106178665559 chr4 191154276 1057040 0.005529774285561888 0.07810920765413064 chr5 180915260 1766340 0.009763355506882062 0.10187628821322861 chr6 171115067 931460 0.0054434715558975295 0.08041921116351719 chr7 159138663 1255039 0.007886449316216763 0.12336375252526494 chr8 146364022 1065640 0.0072807510031392825 0.0945327991682751 chr9 141213431 693251 0.004909242662618969 0.08297447216478222 chr10 135534747 1065084 0.007858383356114577 0.1228625015406826 chr11 135006516 1032084 0.0076446976825918535 0.10349629563757855 chr12 133851895 966184 0.007218306472239336 0.0875650108424548 chr13 115169878 727744 0.006318874454308269 0.0819808372400067 chr14 107349540 535223 0.004985796865082049 0.07414990238962443 chr15 102531392 1039988 0.010143117924313366 0.10410970607976458 chr16 90354753 696756 0.007711337554096352 0.0959054608537224 chr17 81195210 886755 0.010921272326286242 0.110439519624626 chr18 78077248 780756 0.009999788926986771 0.14826277653579278 chr19 59128983 376708 0.006370953479785032 0.10653865451801471 chr20 63025520 610997 0.0096944380625499 0.10120107534310403 chr21 48129895 304392 0.006324385291096106 0.0828503420620144 chr22 51304566 263602 0.005137983235254343 0.07381179730106083 chrMT 16571 55 0.0033190513547764165 0.05751552184307097 chrX 155270560 917841 0.005911236489389875 0.08602858227889792 chrY 59373566 55797 9.397616440959602E-4 0.03452592815671785