BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438286.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 = 587,328,756 number of mapped reads = 585,452,070 (99.68%) number of supplementary alignments = 11,637,960 (1.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 292,943,600 number of mapped paired reads (second in pair) = 292,508,470 number of mapped paired reads (both in pair) = 584,038,914 number of mapped paired reads (singletons) = 1,413,156 number of mapped bases = 84,805,590,694 bp number of sequenced bases = 84,780,980,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,207,271 duplication rate = 50.5% >>>>>>> Insert size mean insert size = 58,849.5347 std insert size = 2,384,599.6817 median insert size = 257 >>>>>>> Mapping quality mean mapping quality = 54.2888 >>>>>>> ACTG content number of A's = 25,796,091,821 bp (30.43%) number of C's = 16,782,161,596 bp (19.79%) number of T's = 24,574,659,699 bp (28.99%) number of G's = 17,627,433,960 bp (20.79%) number of N's = 633,898 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 429,938,247 number of insertions = 10,956,567 mapped reads with insertion percentage = 1.84% number of deletions = 9,807,867 mapped reads with deletion percentage = 1.64% homopolymer indels = 48.72% >>>>>>> Coverage mean coverageData = 27.3947X std coverageData = 156.1234X There is a 60.54% of reference with a coverageData >= 1X There is a 58.53% of reference with a coverageData >= 2X There is a 56.84% of reference with a coverageData >= 3X There is a 55.56% of reference with a coverageData >= 4X There is a 54.32% of reference with a coverageData >= 5X There is a 53.25% of reference with a coverageData >= 6X There is a 52.21% of reference with a coverageData >= 7X There is a 51.24% of reference with a coverageData >= 8X There is a 50.29% of reference with a coverageData >= 9X There is a 49.39% of reference with a coverageData >= 10X There is a 48.49% of reference with a coverageData >= 11X There is a 47.61% of reference with a coverageData >= 12X There is a 46.74% of reference with a coverageData >= 13X There is a 45.89% of reference with a coverageData >= 14X There is a 45.04% of reference with a coverageData >= 15X There is a 44.19% of reference with a coverageData >= 16X There is a 43.35% of reference with a coverageData >= 17X There is a 42.52% of reference with a coverageData >= 18X There is a 41.68% of reference with a coverageData >= 19X There is a 40.86% of reference with a coverageData >= 20X There is a 40.03% of reference with a coverageData >= 21X There is a 39.22% of reference with a coverageData >= 22X There is a 38.4% of reference with a coverageData >= 23X There is a 37.6% of reference with a coverageData >= 24X There is a 36.8% of reference with a coverageData >= 25X There is a 36.01% of reference with a coverageData >= 26X There is a 35.23% of reference with a coverageData >= 27X There is a 34.45% of reference with a coverageData >= 28X There is a 33.68% of reference with a coverageData >= 29X There is a 32.93% of reference with a coverageData >= 30X There is a 32.18% of reference with a coverageData >= 31X There is a 31.45% of reference with a coverageData >= 32X There is a 30.72% of reference with a coverageData >= 33X There is a 30.01% of reference with a coverageData >= 34X There is a 29.31% of reference with a coverageData >= 35X There is a 28.62% of reference with a coverageData >= 36X There is a 27.94% of reference with a coverageData >= 37X There is a 27.27% of reference with a coverageData >= 38X There is a 26.62% of reference with a coverageData >= 39X There is a 25.97% of reference with a coverageData >= 40X There is a 25.35% of reference with a coverageData >= 41X There is a 24.73% of reference with a coverageData >= 42X There is a 24.13% of reference with a coverageData >= 43X There is a 23.53% of reference with a coverageData >= 44X There is a 22.96% of reference with a coverageData >= 45X There is a 22.39% of reference with a coverageData >= 46X There is a 21.84% of reference with a coverageData >= 47X There is a 21.29% of reference with a coverageData >= 48X There is a 20.77% of reference with a coverageData >= 49X There is a 20.25% of reference with a coverageData >= 50X There is a 19.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7338007882 29.44027923605454 47.56534438992705 chr2 243199373 6928542026 28.4891442791672 114.98230146170293 chr3 198022430 5463577627 27.590700846363717 111.21383002287133 chr4 191154276 7962304650 41.653813959149936 46.62301695762246 chr5 180915260 5604116751 30.976473466085725 44.749329042773866 chr6 171115067 5577033311 32.592298321690166 41.891965028286585 chr7 159138663 3554388829 22.335168349378428 36.02492594772187 chr8 146364022 4425073015 30.233338456632463 41.68255160336801 chr9 141213431 3726789393 26.39118224526391 43.62090414154689 chr10 135534747 3770709117 27.82097728046078 44.70811776858165 chr11 135006516 3359867019 24.886702646263384 37.63788457354678 chr12 133851895 4308639887 32.18960693085443 45.85371294341128 chr13 115169878 2769351370 24.04579581129712 38.81751611863574 chr14 107349540 2990378302 27.856461257309533 40.931599568438784 chr15 102531392 1532128490 14.943018524511986 29.07062105802536 chr16 90354753 1706332296 18.88480947980678 46.462362056280696 chr17 81195210 1828742131 22.52278343759441 39.01585482706048 chr18 78077248 2222610685 28.466816414943313 42.97548291067027 chr19 59128983 1271343412 21.501188545725537 128.46064561695522 chr20 63025520 2168718298 34.410161122034374 45.16336250982974 chr21 48129895 1132498657 23.53004628412341 49.645550554118174 chr22 51304566 1105204366 21.54202738992081 38.86916071685846 chrMT 16571 957917608 57806.86790175608 23044.965300207736 chrX 155270560 2719206466 17.512698260378528 35.928878670656296 chrY 59373566 382109106 6.435677217029545 22.14943490735028