BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438271.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 = 1,310,430,866 number of mapped reads = 1,303,468,623 (99.47%) number of supplementary alignments = 13,397,829 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 651,939,697 number of mapped paired reads (second in pair) = 651,528,926 number of mapped paired reads (both in pair) = 1,301,544,676 number of mapped paired reads (singletons) = 1,923,947 number of mapped bases = 172,663,862,979 bp number of sequenced bases = 172,619,385,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 440,274,808 duplication rate = 30.89% >>>>>>> Insert size mean insert size = 37,101.3711 std insert size = 1,919,093.5251 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.4831 >>>>>>> ACTG content number of A's = 50,050,894,590 bp (28.99%) number of C's = 36,550,476,902 bp (21.17%) number of T's = 49,450,809,064 bp (28.65%) number of G's = 36,565,852,514 bp (21.18%) number of N's = 1,351,978 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 737,304,507 number of insertions = 16,682,380 mapped reads with insertion percentage = 1.24% number of deletions = 19,198,649 mapped reads with deletion percentage = 1.44% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 55.7755X std coverageData = 785.9554X There is a 92.35% of reference with a coverageData >= 1X There is a 92.31% of reference with a coverageData >= 2X There is a 92.28% of reference with a coverageData >= 3X There is a 92.24% of reference with a coverageData >= 4X There is a 92.21% of reference with a coverageData >= 5X There is a 92.17% of reference with a coverageData >= 6X There is a 92.13% of reference with a coverageData >= 7X There is a 92.08% of reference with a coverageData >= 8X There is a 92.04% of reference with a coverageData >= 9X There is a 91.99% of reference with a coverageData >= 10X There is a 91.93% of reference with a coverageData >= 11X There is a 91.86% of reference with a coverageData >= 12X There is a 91.79% of reference with a coverageData >= 13X There is a 91.7% of reference with a coverageData >= 14X There is a 91.6% of reference with a coverageData >= 15X There is a 91.47% of reference with a coverageData >= 16X There is a 91.33% of reference with a coverageData >= 17X There is a 91.16% of reference with a coverageData >= 18X There is a 90.96% of reference with a coverageData >= 19X There is a 90.73% of reference with a coverageData >= 20X There is a 90.47% of reference with a coverageData >= 21X There is a 90.17% of reference with a coverageData >= 22X There is a 89.85% of reference with a coverageData >= 23X There is a 89.49% of reference with a coverageData >= 24X There is a 89.11% of reference with a coverageData >= 25X There is a 88.69% of reference with a coverageData >= 26X There is a 88.24% of reference with a coverageData >= 27X There is a 87.77% of reference with a coverageData >= 28X There is a 87.27% of reference with a coverageData >= 29X There is a 86.74% of reference with a coverageData >= 30X There is a 86.18% of reference with a coverageData >= 31X There is a 85.59% of reference with a coverageData >= 32X There is a 84.97% of reference with a coverageData >= 33X There is a 84.3% of reference with a coverageData >= 34X There is a 83.6% of reference with a coverageData >= 35X There is a 82.84% of reference with a coverageData >= 36X There is a 82.03% of reference with a coverageData >= 37X There is a 81.15% of reference with a coverageData >= 38X There is a 80.21% of reference with a coverageData >= 39X There is a 79.18% of reference with a coverageData >= 40X There is a 78.08% of reference with a coverageData >= 41X There is a 76.89% of reference with a coverageData >= 42X There is a 75.61% of reference with a coverageData >= 43X There is a 74.24% of reference with a coverageData >= 44X There is a 72.77% of reference with a coverageData >= 45X There is a 71.2% of reference with a coverageData >= 46X There is a 69.54% of reference with a coverageData >= 47X There is a 67.78% of reference with a coverageData >= 48X There is a 65.94% of reference with a coverageData >= 49X There is a 64.01% of reference with a coverageData >= 50X There is a 62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14747770362 59.168439792974475 2181.3166322894062 chr2 243199373 15010736642 61.72193808246372 508.6192996199787 chr3 198022430 11445470746 57.798860189726994 75.54098736365479 chr4 191154276 10747959106 56.22662140186704 74.30335317313758 chr5 180915260 10375621386 57.350725339587164 38.57955699442774 chr6 171115067 9704440184 56.71294967847571 250.4520094600949 chr7 159138663 9571987921 60.14872652914019 579.6994036867591 chr8 146364022 8610507792 58.82940134017361 200.21245528642234 chr9 141213431 7713046025 54.619776393649126 991.020991071427 chr10 135534747 9217644024 68.00945313307739 1472.1567473379027 chr11 135006516 8140565149 60.29757222236592 253.96806451447418 chr12 133851895 7785505024 58.16507135741335 36.76917008593164 chr13 115169878 5438485175 47.2214199532277 27.62775447878371 chr14 107349540 5286577802 49.24639455371676 46.30321635236273 chr15 102531392 4897765259 47.76844597018638 34.39245488115589 chr16 90354753 5561049553 61.54684029737761 369.21571606373 chr17 81195210 4966469771 61.16702907720788 291.64663183266515 chr18 78077248 4724982001 60.51675900513297 673.813543408828 chr19 59128983 3982566764 67.35388572470458 1178.7877920357216 chr20 63025520 3848986782 61.07028997142745 64.12604000145096 chr21 48129895 2260634533 46.96944659862649 106.4511278161162 chr22 51304566 2331920505 45.45249452066313 37.01969968275205 chrMT 16571 264857128 15983.171082010742 2034.5943599687523 chrX 155270560 4658602882 30.003130548379552 104.5166201270498 chrY 59373566 1369710463 23.06936495948382 295.5862360138015