BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438293.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 = 691,439,774 number of mapped reads = 689,357,538 (99.7%) number of supplementary alignments = 11,498,675 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 344,826,838 number of mapped paired reads (second in pair) = 344,530,700 number of mapped paired reads (both in pair) = 687,944,886 number of mapped paired reads (singletons) = 1,412,652 number of mapped bases = 99,031,287,875 bp number of sequenced bases = 99,005,238,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 285,490,518 duplication rate = 38.67% >>>>>>> Insert size mean insert size = 38,310.2726 std insert size = 1,901,928.3749 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.0515 >>>>>>> ACTG content number of A's = 29,954,007,265 bp (30.25%) number of C's = 19,792,788,026 bp (19.99%) number of T's = 28,648,661,276 bp (28.94%) number of G's = 20,609,170,701 bp (20.82%) number of N's = 611,337 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 504,496,936 number of insertions = 12,063,270 mapped reads with insertion percentage = 1.72% number of deletions = 10,654,922 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 31.99X std coverageData = 92.1862X There is a 91.56% of reference with a coverageData >= 1X There is a 90.94% of reference with a coverageData >= 2X There is a 90.21% of reference with a coverageData >= 3X There is a 89.41% of reference with a coverageData >= 4X There is a 88.49% of reference with a coverageData >= 5X There is a 87.48% of reference with a coverageData >= 6X There is a 86.36% of reference with a coverageData >= 7X There is a 85.13% of reference with a coverageData >= 8X There is a 83.8% of reference with a coverageData >= 9X There is a 82.38% of reference with a coverageData >= 10X There is a 80.86% of reference with a coverageData >= 11X There is a 79.27% of reference with a coverageData >= 12X There is a 77.6% of reference with a coverageData >= 13X There is a 75.86% of reference with a coverageData >= 14X There is a 74.07% of reference with a coverageData >= 15X There is a 72.22% of reference with a coverageData >= 16X There is a 70.34% of reference with a coverageData >= 17X There is a 68.43% of reference with a coverageData >= 18X There is a 66.5% of reference with a coverageData >= 19X There is a 64.55% of reference with a coverageData >= 20X There is a 62.59% of reference with a coverageData >= 21X There is a 60.64% of reference with a coverageData >= 22X There is a 58.69% of reference with a coverageData >= 23X There is a 56.75% of reference with a coverageData >= 24X There is a 54.83% of reference with a coverageData >= 25X There is a 52.93% of reference with a coverageData >= 26X There is a 51.06% of reference with a coverageData >= 27X There is a 49.22% of reference with a coverageData >= 28X There is a 47.41% of reference with a coverageData >= 29X There is a 45.64% of reference with a coverageData >= 30X There is a 43.91% of reference with a coverageData >= 31X There is a 42.22% of reference with a coverageData >= 32X There is a 40.58% of reference with a coverageData >= 33X There is a 38.97% of reference with a coverageData >= 34X There is a 37.42% of reference with a coverageData >= 35X There is a 35.91% of reference with a coverageData >= 36X There is a 34.44% of reference with a coverageData >= 37X There is a 33.02% of reference with a coverageData >= 38X There is a 31.65% of reference with a coverageData >= 39X There is a 30.32% of reference with a coverageData >= 40X There is a 29.04% of reference with a coverageData >= 41X There is a 27.81% of reference with a coverageData >= 42X There is a 26.62% of reference with a coverageData >= 43X There is a 25.47% of reference with a coverageData >= 44X There is a 24.37% of reference with a coverageData >= 45X There is a 23.31% of reference with a coverageData >= 46X There is a 22.29% of reference with a coverageData >= 47X There is a 21.31% of reference with a coverageData >= 48X There is a 20.37% of reference with a coverageData >= 49X There is a 19.47% of reference with a coverageData >= 50X There is a 18.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7949770601 31.89468723931484 30.235312083128708 chr2 243199373 8743040081 35.95009301689277 116.8585263245917 chr3 198022430 7212501051 36.422646924391344 188.06409422798447 chr4 191154276 6742010447 35.2699954616762 31.909692924282997 chr5 180915260 6500823444 35.932974609217595 43.52870087266247 chr6 171115067 5900015933 34.47981546242214 30.48230064217321 chr7 159138663 5359629298 33.67898910901369 30.57934007793082 chr8 146364022 5246808295 35.84766408646518 26.764952664675917 chr9 141213431 4179249408 29.595268512383925 32.91097754001954 chr10 135534747 4738278329 34.95987880510081 38.86255263272709 chr11 135006516 4730349603 35.03793552453424 26.98996879287615 chr12 133851895 4692736567 35.05917168374792 26.598142289755064 chr13 115169878 3460430240 30.04631332508662 26.041760756203317 chr14 107349540 3140961765 29.259200970958982 29.2575901880211 chr15 102531392 2891153722 28.1977418389092 28.67503476683469 chr16 90354753 2713806992 30.03502197609903 50.08680333514425 chr17 81195210 2339725981 28.816059235514015 34.662921168977064 chr18 78077248 2677826897 34.29714757620555 26.496914657106874 chr19 59128983 1528703197 25.85370353824621 271.26532629310174 chr20 63025520 2178156597 34.5599147297793 30.27294773079372 chr21 48129895 1251021997 25.99261845470471 97.61063964468698 chr22 51304566 1056801933 20.598594148520817 26.36525357228305 chrMT 16571 350192464 21132.850401303484 7878.297167250927 chrX 155270560 2951559826 19.009140084250355 33.61252857885686 chrY 59373566 495733207 8.349392505749107 26.618433203092717