BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716901.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 = 804,518 number of mapped reads = 655,264 (81.45%) number of supplementary alignments = 2,422 (0.3%) number of secondary alignments = 0 number of mapped bases = 36,345,063 bp number of sequenced bases = 36,334,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,132 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8778 >>>>>>> ACTG content number of A's = 8,391,820 bp (23.1%) number of C's = 8,135,097 bp (22.39%) number of T's = 10,845,500 bp (29.85%) number of G's = 8,961,166 bp (24.66%) number of N's = 913 bp (0%) GC percentage = 47.05% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 198,531 number of insertions = 2,699 mapped reads with insertion percentage = 0.41% number of deletions = 6,371 mapped reads with deletion percentage = 0.96% homopolymer indels = 34.91% >>>>>>> Coverage mean coverageData = 0.0117X std coverageData = 0.1279X There is a 1.09% of reference with a coverageData >= 1X There is a 0.06% 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 3517471 0.014112185501836724 0.14863403210331888 chr2 243199373 3155308 0.012974161738484416 0.1530551060322965 chr3 198022430 2388523 0.01206188107074537 0.11856348309725008 chr4 191154276 2082688 0.010895325197956858 0.12319495825841419 chr5 180915260 2212341 0.012228603601487238 0.11836644418093233 chr6 171115067 1540773 0.009004309363359568 0.1026255190315086 chr7 159138663 2059292 0.012940236905220198 0.13867084133968824 chr8 146364022 2201309 0.015039959751857597 0.1357398384458049 chr9 141213431 1557687 0.011030728373138954 0.11737866325867638 chr10 135534747 1857999 0.013708654357100029 0.17178650302080314 chr11 135006516 1481333 0.010972307440331251 0.13134455772388734 chr12 133851895 1751970 0.013088869604722443 0.12272510348062844 chr13 115169878 623719 0.005415643489697888 0.07840490661537096 chr14 107349540 1662264 0.0154845935995627 0.13381993192796654 chr15 102531392 728311 0.007103297690525844 0.09012026065993321 chr16 90354753 986739 0.010920720462818376 0.11730795045460268 chr17 81195210 1475172 0.018168214602807233 0.1483358303435616 chr18 78077248 945155 0.012105383120060789 0.13654270894522022 chr19 59128983 979660 0.01656818619728332 0.1508205967256727 chr20 63025520 946208 0.015013093108950153 0.1346833833440556 chr21 48129895 517545 0.010753088075508996 0.11845243253436974 chr22 51304566 413636 0.00806236232463208 0.09738801435061349 chrMT 16571 5748 0.3468710397682699 0.6350968096331067 chrX 155270560 1136565 0.007319900179402972 0.09646891473113609 chrY 59373566 117647 0.0019814710135483524 0.07196508513721701