BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354860.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 20,614,402 number of mapped reads = 20,269,240 (98.33%) number of supplementary alignments = 647,570 (3.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,163,037 number of mapped paired reads (second in pair) = 10,106,203 number of mapped paired reads (both in pair) = 20,190,438 number of mapped paired reads (singletons) = 78,802 number of mapped bases = 2,630,969,984 bp number of sequenced bases = 2,629,723,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,550,877 duplication rate = 64.93% >>>>>>> Insert size mean insert size = 306,832.6608 std insert size = 6,372,744.7408 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 53.5962 >>>>>>> ACTG content number of A's = 731,768,113 bp (27.83%) number of C's = 563,793,441 bp (21.44%) number of T's = 741,462,144 bp (28.2%) number of G's = 592,679,676 bp (22.54%) number of N's = 20,188 bp (0%) GC percentage = 43.98% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 18,114,710 number of insertions = 401,169 mapped reads with insertion percentage = 1.82% number of deletions = 410,311 mapped reads with deletion percentage = 1.91% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.8499X std coverageData = 30.9931X There is a 19.35% of reference with a coverageData >= 1X There is a 14.06% of reference with a coverageData >= 2X There is a 9.61% of reference with a coverageData >= 3X There is a 7.74% of reference with a coverageData >= 4X There is a 5.51% of reference with a coverageData >= 5X There is a 4.69% of reference with a coverageData >= 6X There is a 3.38% of reference with a coverageData >= 7X There is a 2.98% of reference with a coverageData >= 8X There is a 2.14% of reference with a coverageData >= 9X There is a 1.92% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.24% of reference with a coverageData >= 12X There is a 0.88% of reference with a coverageData >= 13X There is a 0.8% of reference with a coverageData >= 14X There is a 0.57% of reference with a coverageData >= 15X There is a 0.52% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.34% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214831031 0.8619077061396769 30.363375808359237 chr2 243199373 243127145 0.9997030091027413 98.4135831900604 chr3 198022430 167202869 0.8443632824826965 2.8188093820568754 chr4 191154276 172402947 0.9019047368838351 15.104735897865972 chr5 180915260 153805460 0.8501519440648622 2.55038186060498 chr6 171115067 145797932 0.8520461380528227 4.297975972674201 chr7 159138663 139587898 0.8771463538059259 15.420169503941146 chr8 146364022 128303339 0.8766043543132478 6.295679894671002 chr9 141213431 112338061 0.7955196627153688 13.955617279011657 chr10 135534747 151752471 1.1196573156254905 33.020046042503814 chr11 135006516 119369641 0.8841768866918986 5.4900820092251905 chr12 133851895 113456478 0.8476269835402779 2.5501460312509323 chr13 115169878 78690763 0.6832581953416674 2.2241021153013567 chr14 107349540 73131706 0.6812484338544906 4.439117112395977 chr15 102531392 73154847 0.7134873093305902 2.2841236057943615 chr16 90354753 82293971 0.9107874048418902 5.927584735139717 chr17 81195210 73306701 0.9028451432048763 5.643720109041128 chr18 78077248 74599393 0.9554562297072766 15.609063260368865 chr19 59128983 55200192 0.9335555796723242 18.240681124496444 chr20 63025520 56840242 0.9018607383167961 5.427430278200169 chr21 48129895 36336341 0.754964061317815 8.2275942881081 chr22 51304566 35693642 0.6957205719272628 2.893713564936272 chrMT 16571 24581166 1483.3845875324362 412.2097378498997 chrX 155270560 67583193 0.4352608311582054 2.3363448810759615 chrY 59373566 37582555 0.6329846349468045 19.10136382363852