BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716961.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 = 1,833,011 number of mapped reads = 1,734,319 (94.62%) number of supplementary alignments = 38,135 (2.08%) number of secondary alignments = 0 number of mapped bases = 135,611,601 bp number of sequenced bases = 135,559,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,252 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0672 >>>>>>> ACTG content number of A's = 33,730,485 bp (24.88%) number of C's = 27,183,104 bp (20.05%) number of T's = 39,701,138 bp (29.29%) number of G's = 34,938,780 bp (25.77%) number of N's = 5,760 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 868,049 number of insertions = 10,889 mapped reads with insertion percentage = 0.62% number of deletions = 24,569 mapped reads with deletion percentage = 1.39% homopolymer indels = 39.06% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.3407X There is a 3.63% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 11083160 0.04446592732862238 0.4721253977043592 chr2 243199373 11430067 0.046998751925236254 0.40017693389417286 chr3 198022430 8848456 0.044684109774837125 0.2453628606256647 chr4 191154276 8568829 0.04482677123058445 0.3671984296525992 chr5 180915260 7942435 0.04390140997503472 0.24526134143129158 chr6 171115067 7577044 0.04428040226288197 0.2558733943701837 chr7 159138663 7388758 0.04642968503511934 0.4105919132837886 chr8 146364022 6849761 0.046799486010298354 0.36168467681893435 chr9 141213431 5627048 0.039847824390018535 0.30940039730056135 chr10 135534747 6642917 0.04901264913269805 0.4671935073354061 chr11 135006516 6171148 0.045710001138019145 0.37517746714060696 chr12 133851895 6032013 0.04506483079675488 0.25064563185314687 chr13 115169878 4011359 0.034829931833391364 0.21682556151692967 chr14 107349540 4073650 0.03794753102807893 0.25147120844877535 chr15 102531392 3964464 0.03866585562400245 0.2309458671128091 chr16 90354753 4228479 0.04679863382505179 0.2798181899636012 chr17 81195210 3894922 0.047969849452941866 0.29532585226774316 chr18 78077248 3555417 0.04553717108471856 0.46434208178399855 chr19 59128983 2908086 0.04918207370486991 0.3781761515317258 chr20 63025520 3134353 0.04973148972035455 0.28707958724080124 chr21 48129895 1872893 0.038913299104433946 0.30586399410804244 chr22 51304566 1857931 0.03621375532150491 0.2297934952728872 chrMT 16571 43145 2.6036449218514273 2.487724868460943 chrX 155270560 7411926 0.04773555270232812 0.278450545434605 chrY 59373566 493340 0.00830908488804597 0.3358751361520132