BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716808.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 = 999,823 number of mapped reads = 918,628 (91.88%) number of supplementary alignments = 3,855 (0.39%) number of secondary alignments = 0 number of mapped bases = 53,338,349 bp number of sequenced bases = 53,322,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,091 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8261 >>>>>>> ACTG content number of A's = 13,498,348 bp (25.31%) number of C's = 9,961,092 bp (18.68%) number of T's = 17,209,092 bp (32.27%) number of G's = 12,652,552 bp (23.73%) number of N's = 1,069 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 265,301 number of insertions = 4,493 mapped reads with insertion percentage = 0.49% number of deletions = 10,210 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.79% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1812X There is a 1.6% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4303745 0.01726673732138866 0.2693573508722691 chr2 243199373 4499406 0.01850089473709293 0.25051858343487143 chr3 198022430 3512250 0.01773662710835333 0.14159707835212265 chr4 191154276 3395787 0.017764640535689612 0.15754284571749372 chr5 180915260 3139223 0.017351897236308315 0.13952063287950048 chr6 171115067 3099601 0.018114132521129773 0.15840983931446487 chr7 159138663 2899137 0.01821767850343194 0.2040339758805594 chr8 146364022 2670197 0.018243533919831748 0.20063840085015006 chr9 141213431 2236285 0.015836206118382608 0.15464489709292267 chr10 135534747 2600325 0.019185670520342653 0.19961851449708748 chr11 135006516 2407954 0.01783583541997336 0.1614171162578284 chr12 133851895 2379127 0.017774324375459907 0.14255513496891667 chr13 115169878 1651436 0.014339131278753286 0.1268845280340746 chr14 107349540 1632693 0.015209128981828893 0.13382976012745884 chr15 102531392 1537684 0.014997202027648274 0.1292074046138963 chr16 90354753 1611301 0.017833051903755413 0.1468741739306243 chr17 81195210 1527022 0.018806799071028942 0.15080540622497512 chr18 78077248 1375222 0.017613607487804897 0.23940922150396451 chr19 59128983 1131510 0.019136300720748064 0.20837646209551935 chr20 63025520 1168939 0.01854707426452015 0.1482111221015905 chr21 48129895 703872 0.0146244241754527 0.14320488821172814 chr22 51304566 653944 0.012746311897463473 0.12035721745394894 chrMT 16571 12435 0.7504073381208135 0.9766350335738498 chrX 155270560 2998784 0.019313281281396807 0.154636351642254 chrY 59373566 190470 0.003207993267576349 0.1320888013551827