BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354855.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 = 29,308,442 number of mapped reads = 28,750,751 (98.1%) number of supplementary alignments = 637,295 (2.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,418,141 number of mapped paired reads (second in pair) = 14,332,610 number of mapped paired reads (both in pair) = 28,626,006 number of mapped paired reads (singletons) = 124,745 number of mapped bases = 3,967,256,099 bp number of sequenced bases = 3,965,304,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,882,223 duplication rate = 57.86% >>>>>>> Insert size mean insert size = 182,074.6689 std insert size = 4,844,987.6667 median insert size = 304 >>>>>>> Mapping quality mean mapping quality = 53.9565 >>>>>>> ACTG content number of A's = 1,145,884,991 bp (28.9%) number of C's = 819,180,789 bp (20.66%) number of T's = 1,153,144,030 bp (29.08%) number of G's = 847,074,821 bp (21.36%) number of N's = 19,661 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 30,113,577 number of insertions = 641,665 mapped reads with insertion percentage = 2.08% number of deletions = 682,216 mapped reads with deletion percentage = 2.26% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 1.2815X std coverageData = 30.3346X There is a 37.05% of reference with a coverageData >= 1X There is a 27.29% of reference with a coverageData >= 2X There is a 17.79% of reference with a coverageData >= 3X There is a 12.76% of reference with a coverageData >= 4X There is a 8.09% of reference with a coverageData >= 5X There is a 5.78% of reference with a coverageData >= 6X There is a 3.64% of reference with a coverageData >= 7X There is a 2.61% of reference with a coverageData >= 8X There is a 1.65% of reference with a coverageData >= 9X There is a 1.18% of reference with a coverageData >= 10X There is a 0.76% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 319833559 1.283180590350465 31.21394759439381 chr2 243199373 339301696 1.3951585968932576 93.11224156356785 chr3 198022430 292966052 1.4794589279608377 2.6447412036110287 chr4 191154276 282282795 1.476727598811339 20.29752103115454 chr5 180915260 232011937 1.2824343120641122 2.3693078500548426 chr6 171115067 238880130 1.396020433431499 4.946775804657975 chr7 159138663 232205161 1.4591373122193443 15.640391934929355 chr8 146364022 193634358 1.3229641776310301 7.437807271396264 chr9 141213431 164460237 1.1646217773718706 16.780741698409194 chr10 135534747 209193631 1.5434686353898606 32.90724041941269 chr11 135006516 172564942 1.2781971353145651 7.161692713952433 chr12 133851895 168052816 1.2555131625144342 2.3085167356016467 chr13 115169878 132093800 1.1469474683302174 2.1906919650892314 chr14 107349540 131840419 1.2281414433634275 4.016841424447599 chr15 102531392 110569118 1.07839283016854 2.1231927482780004 chr16 90354753 111056761 1.2291191919920361 6.701227292045932 chr17 81195210 87317855 1.0754064802591188 5.825261293601095 chr18 78077248 101718057 1.3027874266265123 16.81395141989987 chr19 59128983 72739430 1.2301823286898068 17.743107078802613 chr20 63025520 73885419 1.172309550163172 7.448321457411149 chr21 48129895 56573013 1.1754235699039028 11.055191338869298 chr22 51304566 37602443 0.7329258569305508 3.814744754895429 chrMT 16571 35883817 2165.4587532436185 340.5720707818299 chrX 155270560 119749424 0.7712307085129338 2.7662402075576464 chrY 59373566 50839229 0.8562603263546609 22.29870554737101