BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514716.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 104,430,813 number of mapped reads = 103,041,822 (98.67%) number of supplementary alignments = 5,723,999 (5.48%) number of secondary alignments = 0 number of mapped bases = 9,816,304,328 bp number of sequenced bases = 9,808,649,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,672,178 duplication rate = 43.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0112 >>>>>>> ACTG content number of A's = 2,909,387,469 bp (29.66%) number of C's = 1,994,064,040 bp (20.33%) number of T's = 2,868,725,638 bp (29.25%) number of G's = 2,033,754,795 bp (20.73%) number of N's = 2,717,088 bp (0.03%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 59,378,147 number of insertions = 3,229,712 mapped reads with insertion percentage = 2.95% number of deletions = 3,240,404 mapped reads with deletion percentage = 2.95% homopolymer indels = 38.57% >>>>>>> Coverage mean coverageData = 3.171X std coverageData = 329.7768X There is a 10.48% of reference with a coverageData >= 1X There is a 7.13% of reference with a coverageData >= 2X There is a 5.8% of reference with a coverageData >= 3X There is a 5.11% of reference with a coverageData >= 4X There is a 4.65% of reference with a coverageData >= 5X There is a 4.32% of reference with a coverageData >= 6X There is a 4.06% of reference with a coverageData >= 7X There is a 3.85% of reference with a coverageData >= 8X There is a 3.67% of reference with a coverageData >= 9X There is a 3.51% of reference with a coverageData >= 10X There is a 3.37% of reference with a coverageData >= 11X There is a 3.24% of reference with a coverageData >= 12X There is a 3.12% of reference with a coverageData >= 13X There is a 3.01% of reference with a coverageData >= 14X There is a 2.92% of reference with a coverageData >= 15X There is a 2.83% of reference with a coverageData >= 16X There is a 2.74% of reference with a coverageData >= 17X There is a 2.66% of reference with a coverageData >= 18X There is a 2.59% of reference with a coverageData >= 19X There is a 2.52% of reference with a coverageData >= 20X There is a 2.45% of reference with a coverageData >= 21X There is a 2.39% of reference with a coverageData >= 22X There is a 2.33% of reference with a coverageData >= 23X There is a 2.27% of reference with a coverageData >= 24X There is a 2.22% of reference with a coverageData >= 25X There is a 2.17% of reference with a coverageData >= 26X There is a 2.12% of reference with a coverageData >= 27X There is a 2.07% of reference with a coverageData >= 28X There is a 2.03% of reference with a coverageData >= 29X There is a 1.99% of reference with a coverageData >= 30X There is a 1.95% of reference with a coverageData >= 31X There is a 1.91% of reference with a coverageData >= 32X There is a 1.87% of reference with a coverageData >= 33X There is a 1.83% of reference with a coverageData >= 34X There is a 1.8% of reference with a coverageData >= 35X There is a 1.76% of reference with a coverageData >= 36X There is a 1.73% of reference with a coverageData >= 37X There is a 1.7% of reference with a coverageData >= 38X There is a 1.66% of reference with a coverageData >= 39X There is a 1.63% of reference with a coverageData >= 40X There is a 1.61% of reference with a coverageData >= 41X There is a 1.58% of reference with a coverageData >= 42X There is a 1.55% of reference with a coverageData >= 43X There is a 1.52% of reference with a coverageData >= 44X There is a 1.5% of reference with a coverageData >= 45X There is a 1.47% of reference with a coverageData >= 46X There is a 1.45% of reference with a coverageData >= 47X There is a 1.42% of reference with a coverageData >= 48X There is a 1.4% of reference with a coverageData >= 49X There is a 1.38% of reference with a coverageData >= 50X There is a 1.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 823744172 3.3048831280544735 57.794684078158724 chr2 243199373 604483790 2.4855483077252836 57.155225028846175 chr3 198022430 552029772 2.787713351462256 27.379047368043455 chr4 191154276 870150844 4.552086734382024 36.036334776818904 chr5 180915260 537362933 2.9702465839531724 27.63064423453352 chr6 171115067 491802301 2.874102845659991 47.380742437185276 chr7 159138663 946241087 5.946016317857339 995.4162821127127 chr8 146364022 607668565 4.151761865357868 36.28190990204194 chr9 141213431 431335591 3.0544940941205514 28.235111254943455 chr10 135534747 329080518 2.4280158799425804 50.132831421684365 chr11 135006516 400066993 2.963316178013215 34.597646484392264 chr12 133851895 458938336 3.4287025671171856 30.624855746515262 chr13 115169878 257553731 2.236294207066886 24.52417040390093 chr14 107349540 426497718 3.9729813280988444 34.78306995507167 chr15 102531392 179111100 1.7468903572478562 48.97919420556459 chr16 90354753 556566855 6.15979609838566 1378.9168938444157 chr17 81195210 130390931 1.6058943748036367 21.192334828722338 chr18 78077248 122460943 1.5684587525420979 17.69186078436756 chr19 59128983 188454303 3.1871730822767574 145.0756365890563 chr20 63025520 194225966 3.081703506769956 36.8914538207787 chr21 48129895 76590811 1.5913355098738529 15.787493768373993 chr22 51304566 66972609 1.305392759778925 49.161746219548206 chrMT 16571 5510884 332.56194556755776 167.81142050575681 chrX 155270560 487956252 3.1426192576364764 61.917106456735425 chrY 59373566 71107323 1.1976259435048924 137.8055574426107