BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714266.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 256,614 number of mapped reads = 208,136 (81.11%) number of supplementary alignments = 6,304 (2.46%) number of secondary alignments = 0 number of mapped bases = 26,881,050 bp number of sequenced bases = 26,292,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 170,633 duplication rate = 42.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.212 >>>>>>> ACTG content number of A's = 6,936,279 bp (26.38%) number of C's = 5,790,723 bp (22.02%) number of T's = 6,572,179 bp (25%) number of G's = 6,992,723 bp (26.6%) number of N's = 187 bp (0%) GC percentage = 48.62% >>>>>>> Mismatches and indels general error rate = 0.0442 number of mismatches = 1,079,137 number of insertions = 29,017 mapped reads with insertion percentage = 13.42% number of deletions = 91,223 mapped reads with deletion percentage = 41.61% homopolymer indels = 31.09% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 2.2573X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 2381144 0.00955321190553824 3.009315729476793 chr2 243199373 3501221 0.014396505043621145 4.766609325529199 chr3 198022430 848881 0.0042867921578378775 0.7622588225133421 chr4 191154276 993497 0.005197356924414288 1.2264409914548113 chr5 180915260 1459360 0.008066538997318413 1.6311119036583872 chr6 171115067 1064938 0.006223519755861125 1.3454770464157313 chr7 159138663 725843 0.004561072628843187 0.6579978095292058 chr8 146364022 1013296 0.0069231221317490165 1.253592603542988 chr9 141213431 1093753 0.007745389317819209 1.3978802298970638 chr10 135534747 1303704 0.009618965090922403 1.4407236534345587 chr11 135006516 1374755 0.010182878876749919 1.6025722263589954 chr12 133851895 1398172 0.01044566459070303 2.511102201591076 chr13 115169878 1077481 0.009355579937316595 3.4503256791951924 chr14 107349540 1127292 0.010501134890750347 3.825835784630987 chr15 102531392 1090431 0.010635094079284518 2.080056803588019 chr16 90354753 490811 0.0054320440674548685 0.6075805470512632 chr17 81195210 971309 0.01196263917538978 1.8642420276700793 chr18 78077248 830464 0.010636440464704904 2.375600876646337 chr19 59128983 670108 0.011332987073361299 1.1604259723942365 chr20 63025520 719014 0.011408299368255907 1.4690613152245122 chr21 48129895 244782 0.005085861915967197 0.7517667662636861 chr22 51304566 154849 0.003018230385186379 0.38958009661583093 chrMT 16571 25514 1.5396777502866454 12.227035718107961 chrX 155270560 2089923 0.013459879322905773 1.413757423109344 chrY 59373566 230508 0.003882333764490413 0.866947412920594