BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438289.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 = 772,820,886 number of mapped reads = 768,371,382 (99.42%) number of supplementary alignments = 18,296,707 (2.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 384,479,059 number of mapped paired reads (second in pair) = 383,892,323 number of mapped paired reads (both in pair) = 765,572,876 number of mapped paired reads (singletons) = 2,798,506 number of mapped bases = 108,462,009,645 bp number of sequenced bases = 108,427,177,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 330,549,125 duplication rate = 38% >>>>>>> Insert size mean insert size = 111,402.4842 std insert size = 3,266,734.6272 median insert size = 488 >>>>>>> Mapping quality mean mapping quality = 54.3126 >>>>>>> ACTG content number of A's = 33,171,213,472 bp (30.59%) number of C's = 20,686,457,970 bp (19.08%) number of T's = 31,101,581,171 bp (28.68%) number of G's = 23,467,724,770 bp (21.64%) number of N's = 200,294 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 613,468,235 number of insertions = 14,302,970 mapped reads with insertion percentage = 1.82% number of deletions = 12,817,899 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 35.0364X std coverageData = 108.6382X There is a 91% of reference with a coverageData >= 1X There is a 90.33% of reference with a coverageData >= 2X There is a 89.6% of reference with a coverageData >= 3X There is a 88.79% of reference with a coverageData >= 4X There is a 87.89% of reference with a coverageData >= 5X There is a 86.91% of reference with a coverageData >= 6X There is a 85.82% of reference with a coverageData >= 7X There is a 84.64% of reference with a coverageData >= 8X There is a 83.38% of reference with a coverageData >= 9X There is a 82.03% of reference with a coverageData >= 10X There is a 80.6% of reference with a coverageData >= 11X There is a 79.11% of reference with a coverageData >= 12X There is a 77.55% of reference with a coverageData >= 13X There is a 75.94% of reference with a coverageData >= 14X There is a 74.28% of reference with a coverageData >= 15X There is a 72.59% of reference with a coverageData >= 16X There is a 70.86% of reference with a coverageData >= 17X There is a 69.12% of reference with a coverageData >= 18X There is a 67.36% of reference with a coverageData >= 19X There is a 65.59% of reference with a coverageData >= 20X There is a 63.81% of reference with a coverageData >= 21X There is a 62.04% of reference with a coverageData >= 22X There is a 60.27% of reference with a coverageData >= 23X There is a 58.51% of reference with a coverageData >= 24X There is a 56.77% of reference with a coverageData >= 25X There is a 55.05% of reference with a coverageData >= 26X There is a 53.35% of reference with a coverageData >= 27X There is a 51.68% of reference with a coverageData >= 28X There is a 50.04% of reference with a coverageData >= 29X There is a 48.42% of reference with a coverageData >= 30X There is a 46.83% of reference with a coverageData >= 31X There is a 45.28% of reference with a coverageData >= 32X There is a 43.76% of reference with a coverageData >= 33X There is a 42.28% of reference with a coverageData >= 34X There is a 40.84% of reference with a coverageData >= 35X There is a 39.43% of reference with a coverageData >= 36X There is a 38.06% of reference with a coverageData >= 37X There is a 36.73% of reference with a coverageData >= 38X There is a 35.43% of reference with a coverageData >= 39X There is a 34.17% of reference with a coverageData >= 40X There is a 32.95% of reference with a coverageData >= 41X There is a 31.76% of reference with a coverageData >= 42X There is a 30.62% of reference with a coverageData >= 43X There is a 29.5% of reference with a coverageData >= 44X There is a 28.43% of reference with a coverageData >= 45X There is a 27.39% of reference with a coverageData >= 46X There is a 26.38% of reference with a coverageData >= 47X There is a 25.41% of reference with a coverageData >= 48X There is a 24.47% of reference with a coverageData >= 49X There is a 23.56% of reference with a coverageData >= 50X There is a 22.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8817471353 35.37592531414395 47.762264886937196 chr2 243199373 9483964778 38.996666237293304 260.5250196652805 chr3 198022430 7876795770 39.777290734186025 29.43569242424389 chr4 191154276 7000119462 36.620260914278475 37.17914838513312 chr5 180915260 6849535449 37.8604626773883 28.847422696811645 chr6 171115067 6526453024 38.14072681279434 34.08337353369459 chr7 159138663 5702360433 35.83265264079792 29.814181740034694 chr8 146364022 5515802607 37.68550858079043 32.417324032049805 chr9 141213431 4476321448 31.69897803842752 56.318666211687905 chr10 135534747 5056704138 37.30928230529696 78.96372413733287 chr11 135006516 5249090637 38.88027624533323 35.01524062428082 chr12 133851895 5033783607 37.60711499078889 30.715112495252402 chr13 115169878 3278580587 28.46734444747784 27.92324943804396 chr14 107349540 3303138809 30.769939107331062 30.570972603354658 chr15 102531392 3916060883 38.19377467341904 37.66275410542205 chr16 90354753 2834021367 31.365492936492227 79.38464961135146 chr17 81195210 2602352929 32.05057205960795 51.19581275814896 chr18 78077248 2793903103 35.78383171240871 68.14777872106855 chr19 59128983 1548592331 26.190072151249414 34.377362301802876 chr20 63025520 2234721837 35.457412124485444 33.09451563447213 chr21 48129895 1419461560 29.492305354083985 45.847392154384465 chr22 51304566 1112319060 21.680703039179786 28.97210443819527 chrMT 16571 464784355 28048.05714802969 10176.369572985697 chrX 155270560 5227402931 33.66641384561246 27.44633635326128 chrY 59373566 138267187 2.328766761289022 39.154168901067926