BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714252.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 = 395,200 number of mapped reads = 55,520 (14.05%) number of supplementary alignments = 1,505 (0.38%) number of secondary alignments = 0 number of mapped bases = 5,625,942 bp number of sequenced bases = 5,605,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,126 duplication rate = 33.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 12.6261 >>>>>>> ACTG content number of A's = 218,085 bp (3.89%) number of C's = 117,127 bp (2.09%) number of T's = 148,378 bp (2.65%) number of G's = 5,122,259 bp (91.37%) number of N's = 129 bp (0%) GC percentage = 93.46% >>>>>>> Mismatches and indels general error rate = 0.0347 number of mismatches = 147,380 number of insertions = 6,882 mapped reads with insertion percentage = 8.33% number of deletions = 3,846 mapped reads with deletion percentage = 6.59% homopolymer indels = 57.99% >>>>>>> Coverage mean coverageData = 0.0018X std coverageData = 6.3766X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 69704 2.796542681432276E-4 0.46323672356688683 chr2 243199373 5098861 0.020965765401048136 22.739994249576032 chr3 198022430 9394 4.7439070412377024E-5 0.019808269193528943 chr4 191154276 8393 4.390694352032177E-5 0.015444179941567453 chr5 180915260 11563 6.391390090587163E-5 0.03474346015969214 chr6 171115067 6334 3.701602734959628E-5 0.014359429533021712 chr7 159138663 10616 6.670911895244464E-5 0.07520040899667776 chr8 146364022 6219 4.248995016001952E-5 0.017004327016860502 chr9 141213431 10289 7.286134135498769E-5 0.03769314465878463 chr10 135534747 48621 3.5873457601245235E-4 0.5794400816840997 chr11 135006516 14302 1.0593562758111617E-4 0.04789282787230848 chr12 133851895 9004 6.726837897961773E-5 0.056090635627987225 chr13 115169878 2620 2.2749003867139636E-5 0.007108693975072225 chr14 107349540 8384 7.810000862602672E-5 0.06736669367363773 chr15 102531392 2891 2.8196242571250764E-5 0.010851198483199329 chr16 90354753 7379 8.16669821453665E-5 0.024628630437832772 chr17 81195210 8251 1.0161929502984228E-4 0.07803508514699628 chr18 78077248 3835 4.9118022192585476E-5 0.026755185125518388 chr19 59128983 4172 7.055761469802381E-5 0.027766661315332085 chr20 63025520 8305 1.3177201869972672E-4 0.03940737341725873 chr21 48129895 2098 4.3590371431311036E-5 0.010017561385450112 chr22 51304566 1144 2.229821026066179E-5 0.006101488894130103 chrMT 16571 3524 0.2126606722587653 0.9254662745975762 chrX 155270560 257798 0.0016603147435032114 0.24475874495676692 chrY 59373566 12241 2.0616918983778067E-4 0.06599748137557088