BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514760.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 = 76,565,125 number of mapped reads = 71,864,445 (93.86%) number of supplementary alignments = 12,055,261 (15.75%) number of secondary alignments = 0 number of mapped bases = 6,747,195,455 bp number of sequenced bases = 6,740,853,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,014,176 duplication rate = 49.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8075 >>>>>>> ACTG content number of A's = 2,056,033,238 bp (30.5%) number of C's = 1,288,052,520 bp (19.11%) number of T's = 2,046,925,102 bp (30.37%) number of G's = 1,349,384,521 bp (20.02%) number of N's = 458,116 bp (0.01%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 38,250,330 number of insertions = 5,118,014 mapped reads with insertion percentage = 6.78% number of deletions = 2,076,954 mapped reads with deletion percentage = 2.67% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 2.1795X std coverageData = 231.9177X There is a 4.58% of reference with a coverageData >= 1X There is a 2.99% of reference with a coverageData >= 2X There is a 2.44% of reference with a coverageData >= 3X There is a 2.14% of reference with a coverageData >= 4X There is a 1.94% of reference with a coverageData >= 5X There is a 1.8% of reference with a coverageData >= 6X There is a 1.69% of reference with a coverageData >= 7X There is a 1.59% of reference with a coverageData >= 8X There is a 1.52% of reference with a coverageData >= 9X There is a 1.45% of reference with a coverageData >= 10X There is a 1.39% of reference with a coverageData >= 11X There is a 1.34% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.25% of reference with a coverageData >= 14X There is a 1.21% of reference with a coverageData >= 15X There is a 1.17% of reference with a coverageData >= 16X There is a 1.14% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 1.08% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 1.03% of reference with a coverageData >= 21X There is a 1% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.96% of reference with a coverageData >= 24X There is a 0.94% of reference with a coverageData >= 25X There is a 0.92% of reference with a coverageData >= 26X There is a 0.9% of reference with a coverageData >= 27X There is a 0.88% of reference with a coverageData >= 28X There is a 0.87% of reference with a coverageData >= 29X There is a 0.85% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.82% of reference with a coverageData >= 32X There is a 0.81% of reference with a coverageData >= 33X There is a 0.79% of reference with a coverageData >= 34X There is a 0.78% of reference with a coverageData >= 35X There is a 0.77% of reference with a coverageData >= 36X There is a 0.75% of reference with a coverageData >= 37X There is a 0.74% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.7% of reference with a coverageData >= 42X There is a 0.69% of reference with a coverageData >= 43X There is a 0.68% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.66% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.64% of reference with a coverageData >= 48X There is a 0.64% of reference with a coverageData >= 49X There is a 0.63% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 372289679 1.4936359135490378 36.10225731713291 chr2 243199373 603350417 2.480888044888175 44.02287110256855 chr3 198022430 390326298 1.9711216451590863 35.964597562626246 chr4 191154276 526765490 2.7557086402817377 47.14774308236488 chr5 180915260 430949556 2.3820519949505643 45.96324176349553 chr6 171115067 441684002 2.581210466989444 53.58887943044888 chr7 159138663 261651277 1.6441716429400943 29.39248380378128 chr8 146364022 280838985 1.918770618369588 38.52533150417251 chr9 141213431 288955233 2.0462305246304795 66.70174325041138 chr10 135534747 730403685 5.389051156010938 1043.818667416124 chr11 135006516 334443462 2.477239409688937 203.73737977508154 chr12 133851895 203741416 1.522140691396263 32.79242483794201 chr13 115169878 339529496 2.9480755028671646 141.83075207783963 chr14 107349540 216366183 2.0155296706441406 97.813110809007 chr15 102531392 149429236 1.4573998566214725 34.293848959531196 chr16 90354753 256255936 2.8361090865911613 84.97232334678728 chr17 81195210 99627343 1.2270101031821952 34.17306765900107 chr18 78077248 129112606 1.653652111303923 36.703603430431066 chr19 59128983 32894469 0.5563171786668477 27.233347119574166 chr20 63025520 93709828 1.486855292903573 29.92423515534504 chr21 48129895 95352491 1.9811489511871987 35.24442482368443 chr22 51304566 135112696 2.6335413499063614 172.67503127808794 chrMT 16571 173887087 10493.45766700863 10470.729610906916 chrX 155270560 131906463 0.8495265490122532 23.797356382236867 chrY 59373566 28612121 0.48189999232992003 14.686744622617482