BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716122.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 = 1,051,760 number of mapped reads = 836,983 (79.58%) number of supplementary alignments = 3,385 (0.32%) number of secondary alignments = 0 number of mapped bases = 46,752,587 bp number of sequenced bases = 46,738,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,791 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3808 >>>>>>> ACTG content number of A's = 12,009,507 bp (25.69%) number of C's = 8,871,480 bp (18.98%) number of T's = 14,955,022 bp (32%) number of G's = 10,902,266 bp (23.33%) number of N's = 688 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 240,733 number of insertions = 3,535 mapped reads with insertion percentage = 0.42% number of deletions = 8,896 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1702X There is a 1.41% of reference with a coverageData >= 1X There is a 0.07% 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 3813125 0.015298357070091312 0.19357607712650626 chr2 243199373 4308622 0.01771641903040597 0.20877837818102224 chr3 198022430 3604996 0.018204988192499202 0.14731092711086408 chr4 191154276 2710326 0.014178735923228837 0.1272893161758512 chr5 180915260 2418861 0.013370132513973669 0.12129482635876185 chr6 171115067 2686465 0.015699757169834728 0.13962736356066538 chr7 159138663 2966076 0.0186383116716269 0.3647013261949387 chr8 146364022 3731057 0.02549162662392538 0.1816836946192526 chr9 141213431 1927860 0.013652100840181413 0.1358697253309522 chr10 135534747 2255358 0.01664044128846162 0.21190916282755928 chr11 135006516 1399866 0.010368877306633112 0.12238142778954722 chr12 133851895 2217363 0.016565794604551546 0.13811473062636812 chr13 115169878 1077023 0.009351603203052799 0.10049477733226579 chr14 107349540 1176889 0.010963148980424137 0.11228210473266022 chr15 102531392 1108676 0.010813039581087517 0.11070624361174013 chr16 90354753 1433845 0.015869060037162628 0.13747266204174857 chr17 81195210 1907796 0.02349641068728069 0.16409251847266573 chr18 78077248 1105626 0.014160668162894265 0.17881992986943573 chr19 59128983 933135 0.015781347025704804 0.18809654450976776 chr20 63025520 1030381 0.01634863147499616 0.1347110264685782 chr21 48129895 481817 0.010010763580514772 0.10525148128120719 chr22 51304566 663337 0.012929395017199833 0.11926907159530292 chrMT 16571 12580 0.7591575644197694 1.035716959029449 chrX 155270560 1679609 0.010817304967535378 0.11854757255821886 chrY 59373566 101898 0.0017162182914868208 0.05205943708123153