BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008734.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 = 1,351,857 number of mapped reads = 1,137,830 (84.17%) number of supplementary alignments = 9,409 (0.7%) number of secondary alignments = 0 number of mapped bases = 71,918,300 bp number of sequenced bases = 71,874,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,102 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6351 >>>>>>> ACTG content number of A's = 18,559,300 bp (25.82%) number of C's = 13,179,436 bp (18.34%) number of T's = 22,853,039 bp (31.8%) number of G's = 17,244,601 bp (23.99%) number of N's = 38,157 bp (0.05%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 640,579 number of insertions = 5,504 mapped reads with insertion percentage = 0.48% number of deletions = 25,896 mapped reads with deletion percentage = 2.25% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2268X There is a 1.94% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 5065979 0.02032484003319695 0.26479684922442953 chr2 243199373 8011882 0.032943678682921605 0.3774235690394573 chr3 198022430 5542633 0.02798992518170795 0.1930685842746421 chr4 191154276 3308754 0.0173093381390014 0.16168446761926528 chr5 180915260 2370989 0.013105522441832712 0.13345957411415016 chr6 171115067 2514862 0.014696905679264351 0.1581341214211917 chr7 159138663 4801639 0.0301726740031742 0.28116859513181147 chr8 146364022 6496117 0.044383291134210565 0.28462326189902526 chr9 141213431 1963081 0.013901517625472891 0.19492790554819825 chr10 135534747 4362873 0.03219007004897423 0.2377659116826679 chr11 135006516 2925681 0.02167066514034034 0.23634598713253133 chr12 133851895 3422790 0.02557147211102241 0.1876264929251003 chr13 115169878 1279353 0.011108399368105608 0.121051091239606 chr14 107349540 2174541 0.020256640130921846 0.16676816687331228 chr15 102531392 1954814 0.019065517027214457 0.1651108766598697 chr16 90354753 1917441 0.021221252190241725 0.18228920440402993 chr17 81195210 2857680 0.035195179617122735 0.2489133510587278 chr18 78077248 1409747 0.018055797765822893 0.2556447715495495 chr19 59128983 1496410 0.025307555179834566 0.22634654715039215 chr20 63025520 2072039 0.03287619047014606 0.2133751237385948 chr21 48129895 1040359 0.02161565073017508 0.17806913845619202 chr22 51304566 1093592 0.02131568562533011 0.1689908615501525 chrMT 16571 144222 8.703276808882988 6.010445632078793 chrX 155270560 3479302 0.02240799543712601 0.18319157114240384 chrY 59373566 211520 0.0035625281459429267 0.11211985840728422