BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714085.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 = 619,972 number of mapped reads = 197,449 (31.85%) number of supplementary alignments = 3,835 (0.62%) number of secondary alignments = 0 number of mapped bases = 25,001,883 bp number of sequenced bases = 24,826,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,014 duplication rate = 35.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.3923 >>>>>>> ACTG content number of A's = 5,798,761 bp (23.36%) number of C's = 4,526,512 bp (18.23%) number of T's = 6,082,629 bp (24.5%) number of G's = 8,418,356 bp (33.91%) number of N's = 360 bp (0%) GC percentage = 52.14% >>>>>>> Mismatches and indels general error rate = 0.0284 number of mismatches = 662,029 number of insertions = 11,416 mapped reads with insertion percentage = 5.09% number of deletions = 59,427 mapped reads with deletion percentage = 29.05% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 0.0081X std coverageData = 16.2892X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% 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 59656 2.39341429765184E-4 0.04318819522435979 chr2 243199373 3919545 0.0161165917150617 16.37154451890928 chr3 198022430 8296024 0.04189436519893226 45.82176549486159 chr4 191154276 116535 6.096384681449658E-4 0.4539599426429869 chr5 180915260 62966 3.4804139794509316E-4 0.0623051380572512 chr6 171115067 49218 2.876310126448421E-4 0.06368532737152144 chr7 159138663 209550 0.0013167761752528988 0.7547165380840706 chr8 146364022 68199 4.6595467293184933E-4 0.15852918236863453 chr9 141213431 257176 0.0018211865413850046 0.9199694346761224 chr10 135534747 874965 0.006455650815506374 5.370975131092815 chr11 135006516 196026 0.001451974362481882 0.69913638599346 chr12 133851895 74233 5.545905793862687E-4 0.16572047384777733 chr13 115169878 269149 0.002336973909098002 2.2552952811542153 chr14 107349540 69207 6.446883703460676E-4 0.16291643163737524 chr15 102531392 25801 2.516400050435285E-4 0.040135990191542834 chr16 90354753 47627 5.271111747712928E-4 0.17942495979869405 chr17 81195210 33132 4.0805362779405336E-4 0.11178255291640872 chr18 78077248 16123 2.0650061846442128E-4 0.03346224800977358 chr19 59128983 17586 2.974175963757063E-4 0.07339422876362306 chr20 63025520 34877 5.533790121842707E-4 0.0959161390476368 chr21 48129895 6089 1.265118072665648E-4 0.01912606954288134 chr22 51304566 6171 1.2028169188683908E-4 0.023984087972363944 chrMT 16571 8940756 539.5423329913705 4422.231267263693 chrX 155270560 1344359 0.008658170615215144 6.597986016956062 chrY 59373566 6913 1.1643228570775082E-4 0.029692737095079594