BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173980.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,082,356 number of mapped reads = 3,996,893 (97.91%) number of supplementary alignments = 553,269 (13.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,997,426 number of mapped paired reads (second in pair) = 1,999,467 number of mapped paired reads (both in pair) = 3,941,366 number of mapped paired reads (singletons) = 55,527 number of mapped bases = 452,640,724 bp number of sequenced bases = 452,328,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,222,674 duplication rate = 64.4% >>>>>>> Insert size mean insert size = 1,063,446.1114 std insert size = 9,582,040.3567 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.4709 >>>>>>> ACTG content number of A's = 135,340,967 bp (29.92%) number of C's = 89,701,490 bp (19.83%) number of T's = 134,157,349 bp (29.66%) number of G's = 93,125,666 bp (20.59%) number of N's = 3,282 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 3,769,401 number of insertions = 49,634 mapped reads with insertion percentage = 1.2% number of deletions = 131,060 mapped reads with deletion percentage = 3.2% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.1462X std coverageData = 2.6292X There is a 3.15% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 1.74% of reference with a coverageData >= 3X There is a 1.4% of reference with a coverageData >= 4X There is a 1.05% of reference with a coverageData >= 5X There is a 0.87% of reference with a coverageData >= 6X There is a 0.66% of reference with a coverageData >= 7X There is a 0.57% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 37205936 0.14927118677068413 1.488554969950962 chr2 243199373 42000479 0.1726997832350497 8.158599699786771 chr3 198022430 30208985 0.1525533496382203 1.1862717119891026 chr4 191154276 32055262 0.16769314645098496 1.5298031663729663 chr5 180915260 27170440 0.15018324048507573 1.172788262351354 chr6 171115067 27129980 0.15854816572055574 1.3222434571537112 chr7 159138663 25835986 0.16234889443554015 1.5310015077318817 chr8 146364022 20728837 0.14162522125826796 1.7589458536307256 chr9 141213431 19341638 0.13696741069905738 1.3757242769043576 chr10 135534747 23224678 0.17135589591649145 1.775846185627899 chr11 135006516 20740818 0.15362827376420854 1.215361711916525 chr12 133851895 18807628 0.14051073389734228 1.1695403714597201 chr13 115169878 15398856 0.13370558576088792 1.1153531759748487 chr14 107349540 14258354 0.1328217521938147 1.1161340526484869 chr15 102531392 13728379 0.13389439792254065 1.127521590630573 chr16 90354753 13406878 0.14838043993103495 1.325300547650564 chr17 81195210 12227949 0.15059938880631013 1.2159558204690055 chr18 78077248 12826123 0.16427478335301982 1.7916617463908566 chr19 59128983 8733875 0.14770886554906584 1.2582480096824231 chr20 63025520 9531682 0.15123527739239598 1.1944038868989646 chr21 48129895 6325849 0.13143284438912656 1.3503814982377178 chr22 51304566 5930168 0.11558752879811907 1.1727756241375957 chrMT 16571 453762 27.382897833564662 26.97091530991155 chrX 155270560 12091018 0.07787064077053628 0.8440976412527765 chrY 59373566 3277164 0.05519567411531253 1.0632419561678856