BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438253.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 = 1,330,220,306 number of mapped reads = 1,325,160,856 (99.62%) number of supplementary alignments = 17,074,614 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 662,897,664 number of mapped paired reads (second in pair) = 662,263,192 number of mapped paired reads (both in pair) = 1,322,809,830 number of mapped paired reads (singletons) = 2,351,026 number of mapped bases = 147,446,809,355 bp number of sequenced bases = 147,412,591,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 840,936,444 duplication rate = 54.99% >>>>>>> Insert size mean insert size = 86,274.64 std insert size = 2,908,220.3333 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 52.4092 >>>>>>> ACTG content number of A's = 45,079,732,827 bp (30.58%) number of C's = 28,921,757,517 bp (19.62%) number of T's = 44,064,573,318 bp (29.89%) number of G's = 29,346,120,985 bp (19.91%) number of N's = 406,455 bp (0%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 473,201,899 number of insertions = 21,925,262 mapped reads with insertion percentage = 1.64% number of deletions = 14,864,600 mapped reads with deletion percentage = 1.11% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 47.6296X std coverageData = 511.8684X There is a 74.01% of reference with a coverageData >= 1X There is a 69.02% of reference with a coverageData >= 2X There is a 62% of reference with a coverageData >= 3X There is a 57.66% of reference with a coverageData >= 4X There is a 53.29% of reference with a coverageData >= 5X There is a 49.98% of reference with a coverageData >= 6X There is a 46.97% of reference with a coverageData >= 7X There is a 44.5% of reference with a coverageData >= 8X There is a 42.31% of reference with a coverageData >= 9X There is a 40.45% of reference with a coverageData >= 10X There is a 38.79% of reference with a coverageData >= 11X There is a 37.35% of reference with a coverageData >= 12X There is a 36.06% of reference with a coverageData >= 13X There is a 34.92% of reference with a coverageData >= 14X There is a 33.88% of reference with a coverageData >= 15X There is a 32.95% of reference with a coverageData >= 16X There is a 32.09% of reference with a coverageData >= 17X There is a 31.31% of reference with a coverageData >= 18X There is a 30.59% of reference with a coverageData >= 19X There is a 29.92% of reference with a coverageData >= 20X There is a 29.3% of reference with a coverageData >= 21X There is a 28.72% of reference with a coverageData >= 22X There is a 28.17% of reference with a coverageData >= 23X There is a 27.66% of reference with a coverageData >= 24X There is a 27.17% of reference with a coverageData >= 25X There is a 26.71% of reference with a coverageData >= 26X There is a 26.28% of reference with a coverageData >= 27X There is a 25.86% of reference with a coverageData >= 28X There is a 25.46% of reference with a coverageData >= 29X There is a 25.08% of reference with a coverageData >= 30X There is a 24.72% of reference with a coverageData >= 31X There is a 24.37% of reference with a coverageData >= 32X There is a 24.03% of reference with a coverageData >= 33X There is a 23.71% of reference with a coverageData >= 34X There is a 23.39% of reference with a coverageData >= 35X There is a 23.09% of reference with a coverageData >= 36X There is a 22.79% of reference with a coverageData >= 37X There is a 22.51% of reference with a coverageData >= 38X There is a 22.23% of reference with a coverageData >= 39X There is a 21.96% of reference with a coverageData >= 40X There is a 21.7% of reference with a coverageData >= 41X There is a 21.45% of reference with a coverageData >= 42X There is a 21.2% of reference with a coverageData >= 43X There is a 20.96% of reference with a coverageData >= 44X There is a 20.72% of reference with a coverageData >= 45X There is a 20.49% of reference with a coverageData >= 46X There is a 20.27% of reference with a coverageData >= 47X There is a 20.05% of reference with a coverageData >= 48X There is a 19.83% of reference with a coverageData >= 49X There is a 19.62% of reference with a coverageData >= 50X There is a 19.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8307733518 33.330843809612816 96.12605349207251 chr2 243199373 12266586150 50.43839545589618 1766.516796503738 chr3 198022430 12320381011 62.2170983913287 156.97921074222592 chr4 191154276 10157020189 53.13519739940319 133.0699331055533 chr5 180915260 10182114000 56.28112299647913 142.32390690183118 chr6 171115067 10816584450 63.212343831767896 164.20959859020363 chr7 159138663 8964299808 56.330118897630804 139.22504879657544 chr8 146364022 7566718420 51.6979399486576 144.72659072914797 chr9 141213431 7398459572 52.392038913069115 156.57454148528552 chr10 135534747 5966949696 44.0252394908001 117.77506021180729 chr11 135006516 5258518657 38.95011005987296 115.64278567032835 chr12 133851895 7346329411 54.884014985368715 150.9390634124287 chr13 115169878 5534117230 48.05177643758553 132.25637255595115 chr14 107349540 5633492938 52.478035192325926 144.69250741656438 chr15 102531392 3477906474 33.92040628883689 108.06498428903717 chr16 90354753 2678035898 29.639125879742043 99.29186699751918 chr17 81195210 2167268153 26.692069064172628 81.77263493228484 chr18 78077248 3783796431 48.46221566364634 124.55401622325456 chr19 59128983 772322196 13.06165194825015 53.58264820958168 chr20 63025520 1678528343 26.632518747961143 76.80134397370516 chr21 48129895 1055139594 21.92274871989644 77.85217849489266 chr22 51304566 999607448 19.48379113079331 81.04151674046999 chrMT 16571 31167 1.8808158831693924 4.534126303026869 chrX 155270560 12954875131 83.4342011196456 210.7707709336683 chrY 59373566 159993470 2.6946919442231243 26.576047695271804