BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438265.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 = 660,138,950 number of mapped reads = 658,207,244 (99.71%) number of supplementary alignments = 10,941,168 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 329,252,461 number of mapped paired reads (second in pair) = 328,954,783 number of mapped paired reads (both in pair) = 656,898,098 number of mapped paired reads (singletons) = 1,309,146 number of mapped bases = 95,250,588,514 bp number of sequenced bases = 95,223,670,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 283,482,250 duplication rate = 40.59% >>>>>>> Insert size mean insert size = 40,672.4745 std insert size = 1,969,837.1769 median insert size = 245 >>>>>>> Mapping quality mean mapping quality = 55.0681 >>>>>>> ACTG content number of A's = 28,800,409,160 bp (30.25%) number of C's = 19,021,219,051 bp (19.98%) number of T's = 27,486,143,815 bp (28.86%) number of G's = 19,915,315,288 bp (20.91%) number of N's = 582,956 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 483,620,717 number of insertions = 12,168,036 mapped reads with insertion percentage = 1.82% number of deletions = 10,800,408 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.42% >>>>>>> Coverage mean coverageData = 30.7687X std coverageData = 85.9921X There is a 91.48% of reference with a coverageData >= 1X There is a 90.8% of reference with a coverageData >= 2X There is a 90.02% of reference with a coverageData >= 3X There is a 89.15% of reference with a coverageData >= 4X There is a 88.15% of reference with a coverageData >= 5X There is a 87.04% of reference with a coverageData >= 6X There is a 85.81% of reference with a coverageData >= 7X There is a 84.46% of reference with a coverageData >= 8X There is a 83.01% of reference with a coverageData >= 9X There is a 81.45% of reference with a coverageData >= 10X There is a 79.79% of reference with a coverageData >= 11X There is a 78.06% of reference with a coverageData >= 12X There is a 76.25% of reference with a coverageData >= 13X There is a 74.37% of reference with a coverageData >= 14X There is a 72.44% of reference with a coverageData >= 15X There is a 70.47% of reference with a coverageData >= 16X There is a 68.47% of reference with a coverageData >= 17X There is a 66.44% of reference with a coverageData >= 18X There is a 64.39% of reference with a coverageData >= 19X There is a 62.35% of reference with a coverageData >= 20X There is a 60.31% of reference with a coverageData >= 21X There is a 58.27% of reference with a coverageData >= 22X There is a 56.26% of reference with a coverageData >= 23X There is a 54.27% of reference with a coverageData >= 24X There is a 52.3% of reference with a coverageData >= 25X There is a 50.37% of reference with a coverageData >= 26X There is a 48.47% of reference with a coverageData >= 27X There is a 46.62% of reference with a coverageData >= 28X There is a 44.81% of reference with a coverageData >= 29X There is a 43.04% of reference with a coverageData >= 30X There is a 41.32% of reference with a coverageData >= 31X There is a 39.66% of reference with a coverageData >= 32X There is a 38.04% of reference with a coverageData >= 33X There is a 36.47% of reference with a coverageData >= 34X There is a 34.95% of reference with a coverageData >= 35X There is a 33.48% of reference with a coverageData >= 36X There is a 32.06% of reference with a coverageData >= 37X There is a 30.69% of reference with a coverageData >= 38X There is a 29.37% of reference with a coverageData >= 39X There is a 28.1% of reference with a coverageData >= 40X There is a 26.88% of reference with a coverageData >= 41X There is a 25.7% of reference with a coverageData >= 42X There is a 24.58% of reference with a coverageData >= 43X There is a 23.49% of reference with a coverageData >= 44X There is a 22.45% of reference with a coverageData >= 45X There is a 21.46% of reference with a coverageData >= 46X There is a 20.5% of reference with a coverageData >= 47X There is a 19.58% of reference with a coverageData >= 48X There is a 18.7% of reference with a coverageData >= 49X There is a 17.86% of reference with a coverageData >= 50X There is a 17.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7744316370 31.07039949962652 30.99562852448959 chr2 243199373 8462095958 34.794892164462944 116.38722859636252 chr3 198022430 6859441648 34.63972060134804 32.43493758577183 chr4 191154276 6421458628 33.59306818749898 24.35436855198194 chr5 180915260 6187713528 34.20227529728559 25.391412351859703 chr6 171115067 5768508591 33.71128382867652 26.517455935966478 chr7 159138663 5188365411 32.602796285903196 25.027049749559357 chr8 146364022 4906674286 33.52377325351171 25.00938187302875 chr9 141213431 4088047636 28.94942504442088 31.93913006081171 chr10 135534747 4541185513 33.50569218238921 38.11939033381232 chr11 135006516 4498110084 33.31772581998931 26.031911444041672 chr12 133851895 4484138438 33.50074676193415 24.799403760816112 chr13 115169878 3263887335 28.339765498405754 25.16850117349954 chr14 107349540 2931710075 27.309945389612288 26.757844897880204 chr15 102531392 2751537892 26.83605321578 26.80951395280632 chr16 90354753 2627589270 29.08080851042778 50.5797872598426 chr17 81195210 2319432622 28.56612627764618 34.44181859790924 chr18 78077248 2627416571 33.651500767547546 26.777685602942878 chr19 59128983 1446940740 24.470922153354135 39.36531829245731 chr20 63025520 2072824035 32.88864629756327 27.8628334714399 chr21 48129895 1218513814 25.317192443490683 30.96684969003725 chr22 51304566 1017345545 19.82953222915871 26.058622357446144 chrMT 16571 495442305 29898.153702250922 11817.949350488374 chrX 155270560 2829312290 18.22182060784736 15.920672346314726 chrY 59373566 498579929 8.39733845529844 27.436760632552108