BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438251.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 830,067,144 number of mapped reads = 825,707,878 (99.47%) number of supplementary alignments = 21,592,174 (2.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 413,095,292 number of mapped paired reads (second in pair) = 412,612,586 number of mapped paired reads (both in pair) = 822,908,678 number of mapped paired reads (singletons) = 2,799,200 number of mapped bases = 116,936,136,673 bp number of sequenced bases = 116,898,666,008 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 346,701,740 duplication rate = 36.79% >>>>>>> Insert size mean insert size = 114,267.3138 std insert size = 3,300,191.0223 median insert size = 466 >>>>>>> Mapping quality mean mapping quality = 54.3252 >>>>>>> ACTG content number of A's = 35,688,081,537 bp (30.53%) number of C's = 22,362,507,051 bp (19.13%) number of T's = 33,568,710,007 bp (28.72%) number of G's = 25,279,151,721 bp (21.62%) number of N's = 215,692 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 627,489,132 number of insertions = 15,520,269 mapped reads with insertion percentage = 1.84% number of deletions = 13,728,931 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 37.7738X std coverageData = 95.9459X There is a 91.09% of reference with a coverageData >= 1X There is a 90.5% of reference with a coverageData >= 2X There is a 89.86% of reference with a coverageData >= 3X There is a 89.16% of reference with a coverageData >= 4X There is a 88.38% of reference with a coverageData >= 5X There is a 87.51% of reference with a coverageData >= 6X There is a 86.55% of reference with a coverageData >= 7X There is a 85.49% of reference with a coverageData >= 8X There is a 84.34% of reference with a coverageData >= 9X There is a 83.11% of reference with a coverageData >= 10X There is a 81.79% of reference with a coverageData >= 11X There is a 80.4% of reference with a coverageData >= 12X There is a 78.95% of reference with a coverageData >= 13X There is a 77.43% of reference with a coverageData >= 14X There is a 75.87% of reference with a coverageData >= 15X There is a 74.26% of reference with a coverageData >= 16X There is a 72.62% of reference with a coverageData >= 17X There is a 70.95% of reference with a coverageData >= 18X There is a 69.27% of reference with a coverageData >= 19X There is a 67.57% of reference with a coverageData >= 20X There is a 65.87% of reference with a coverageData >= 21X There is a 64.16% of reference with a coverageData >= 22X There is a 62.46% of reference with a coverageData >= 23X There is a 60.78% of reference with a coverageData >= 24X There is a 59.1% of reference with a coverageData >= 25X There is a 57.45% of reference with a coverageData >= 26X There is a 55.81% of reference with a coverageData >= 27X There is a 54.2% of reference with a coverageData >= 28X There is a 52.61% of reference with a coverageData >= 29X There is a 51.05% of reference with a coverageData >= 30X There is a 49.52% of reference with a coverageData >= 31X There is a 48.02% of reference with a coverageData >= 32X There is a 46.56% of reference with a coverageData >= 33X There is a 45.12% of reference with a coverageData >= 34X There is a 43.72% of reference with a coverageData >= 35X There is a 42.35% of reference with a coverageData >= 36X There is a 41.01% of reference with a coverageData >= 37X There is a 39.71% of reference with a coverageData >= 38X There is a 38.44% of reference with a coverageData >= 39X There is a 37.21% of reference with a coverageData >= 40X There is a 36.01% of reference with a coverageData >= 41X There is a 34.85% of reference with a coverageData >= 42X There is a 33.71% of reference with a coverageData >= 43X There is a 32.61% of reference with a coverageData >= 44X There is a 31.55% of reference with a coverageData >= 45X There is a 30.51% of reference with a coverageData >= 46X There is a 29.5% of reference with a coverageData >= 47X There is a 28.53% of reference with a coverageData >= 48X There is a 27.59% of reference with a coverageData >= 49X There is a 26.67% of reference with a coverageData >= 50X There is a 25.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9821259466 39.40314943488145 43.12198849317897 chr2 243199373 10400900094 42.7669691977372 173.48589077413774 chr3 198022430 8500469045 42.926798974237414 32.62689429705105 chr4 191154276 7394817254 38.685073694087805 35.7373937040902 chr5 180915260 7641021306 42.2353609419128 33.49831406169972 chr6 171115067 7408943066 43.29801691863873 36.855784857483506 chr7 159138663 6188657465 38.88845958822716 33.16306393102444 chr8 146364022 5809001039 39.68872240337861 33.79486586657044 chr9 141213431 4858318342 34.40408116703857 47.559116107303986 chr10 135534747 5279043992 38.949746163616624 62.03978880999127 chr11 135006516 5479327183 40.58564982893122 36.41138288024136 chr12 133851895 5337550947 39.87654375009035 33.61799268254954 chr13 115169878 3610633006 31.350497792487026 30.828001002442203 chr14 107349540 3646837030 33.9716130129668 34.37751114247244 chr15 102531392 3461167457 33.757148805704304 34.13142763766797 chr16 90354753 3190183623 35.307313860954274 102.61217048938231 chr17 81195210 2931408688 36.10322195114712 48.63522514764834 chr18 78077248 3114981349 39.896146813473756 52.68993414487073 chr19 59128983 1716130052 29.023500235070845 34.15889601331471 chr20 63025520 2387004862 37.87362423983174 35.24162447028389 chr21 48129895 1446254443 30.04898396308573 42.11951405987146 chr22 51304566 1242278993 24.213809605172376 32.129546954955465 chrMT 16571 482798699 29135.157745458935 10882.414328164743 chrX 155270560 5461943197 35.17694015530053 28.303690170964362 chrY 59373566 125206075 2.1087848252200314 33.852379247276254