BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354848.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 19,307,742 number of mapped reads = 19,129,860 (99.08%) number of supplementary alignments = 582,385 (3.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,572,570 number of mapped paired reads (second in pair) = 9,557,290 number of mapped paired reads (both in pair) = 19,102,284 number of mapped paired reads (singletons) = 27,576 number of mapped bases = 2,340,409,829 bp number of sequenced bases = 2,339,441,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,576,652 duplication rate = 78.75% >>>>>>> Insert size mean insert size = 295,867.9912 std insert size = 6,318,495.3064 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 53.8591 >>>>>>> ACTG content number of A's = 676,044,916 bp (28.9%) number of C's = 478,020,177 bp (20.43%) number of T's = 687,541,049 bp (29.39%) number of G's = 497,829,242 bp (21.28%) number of N's = 5,777 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 13,929,359 number of insertions = 340,579 mapped reads with insertion percentage = 1.68% number of deletions = 372,180 mapped reads with deletion percentage = 1.87% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.756X std coverageData = 27.8506X There is a 10.35% of reference with a coverageData >= 1X There is a 9.62% of reference with a coverageData >= 2X There is a 7.24% of reference with a coverageData >= 3X There is a 6.9% of reference with a coverageData >= 4X There is a 5.25% of reference with a coverageData >= 5X There is a 5% of reference with a coverageData >= 6X There is a 3.8% of reference with a coverageData >= 7X There is a 3.62% of reference with a coverageData >= 8X There is a 2.75% of reference with a coverageData >= 9X There is a 2.62% of reference with a coverageData >= 10X There is a 1.99% of reference with a coverageData >= 11X There is a 1.89% of reference with a coverageData >= 12X There is a 1.44% of reference with a coverageData >= 13X There is a 1.37% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 1% of reference with a coverageData >= 16X There is a 0.76% of reference with a coverageData >= 17X There is a 0.73% of reference with a coverageData >= 18X There is a 0.56% of reference with a coverageData >= 19X There is a 0.53% of reference with a coverageData >= 20X There is a 0.41% of reference with a coverageData >= 21X There is a 0.39% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187599211 0.7526529332097431 23.33872338250335 chr2 243199373 220714474 0.9075454071997134 92.33071981741826 chr3 198022430 154526700 0.7803494785918949 3.3590687281037632 chr4 191154276 164225878 0.8591274097368348 7.2925743514573655 chr5 180915260 143576642 0.7936126670574942 3.131751273873127 chr6 171115067 139230494 0.8136658941903696 4.543908553894806 chr7 159138663 129545454 0.8140413621547141 13.850252695784398 chr8 146364022 119526794 0.8166405402551729 4.6051588469056375 chr9 141213431 100210377 0.7096377185255134 11.498434069568715 chr10 135534747 127637039 0.9417292747814698 23.53180222977889 chr11 135006516 105796427 0.7836394133746848 5.139435079542964 chr12 133851895 102182160 0.7633971861212723 3.0756448972303883 chr13 115169878 79003236 0.6859713440002081 2.882120870158002 chr14 107349540 71843425 0.6692476278892299 5.31147260408524 chr15 102531392 61295778 0.5978244984716485 2.6265653347635243 chr16 90354753 65762078 0.7278209038986582 5.300213154373657 chr17 81195210 58583658 0.7215161830359205 4.959083233265436 chr18 78077248 65940923 0.8445600311117523 10.427670447738652 chr19 59128983 40415539 0.6835148678271703 13.005571986044046 chr20 63025520 47775683 0.7580371094121873 3.7407475758891415 chr21 48129895 33283269 0.6915300563194663 5.014073068704811 chr22 51304566 25049996 0.4882605575495951 2.734266541589353 chrMT 16571 9618483 580.440709673526 131.1724775271507 chrX 155270560 62833707 0.40467237961916286 2.6172919709816513 chrY 59373566 24232404 0.4081345560413198 9.279138909053719