BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038444.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 20,137,270 number of mapped reads = 19,449,225 (96.58%) number of supplementary alignments = 272,526 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,851,097 number of mapped paired reads (second in pair) = 9,598,128 number of mapped paired reads (both in pair) = 19,151,432 number of mapped paired reads (singletons) = 297,793 number of mapped bases = 2,653,744,112 bp number of sequenced bases = 2,651,971,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,999,833 duplication rate = 14.41% >>>>>>> Insert size mean insert size = 78,937.2647 std insert size = 2,737,205.6947 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.5543 >>>>>>> ACTG content number of A's = 751,019,330 bp (28.32%) number of C's = 541,135,639 bp (20.41%) number of T's = 761,459,313 bp (28.71%) number of G's = 598,144,564 bp (22.55%) number of N's = 213,072 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 33,958,660 number of insertions = 434,964 mapped reads with insertion percentage = 2.13% number of deletions = 925,749 mapped reads with deletion percentage = 4.59% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.8572X std coverageData = 12.3232X There is a 28.38% of reference with a coverageData >= 1X There is a 17.83% of reference with a coverageData >= 2X There is a 10.96% of reference with a coverageData >= 3X There is a 7.28% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.8% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% 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 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 219994525 0.8826237788992309 17.34124933394673 chr2 243199373 245009891 1.0074445833378032 12.836249125207168 chr3 198022430 187606372 0.9473996051861397 2.20251101830956 chr4 191154276 113185940 0.5921182741420862 9.240510562913045 chr5 180915260 162547077 0.8984707923477544 1.9689697921023654 chr6 171115067 132941333 0.7769119068866098 10.01732239200357 chr7 159138663 132707039 0.8339082187714496 13.286367488306775 chr8 146364022 176906656 1.2086758315510078 4.831276041300751 chr9 141213431 117102918 0.8292618993160785 17.94138539051586 chr10 135534747 148201428 1.0934570748857486 34.80483525989886 chr11 135006516 128914991 0.9548797703956748 10.892611302874462 chr12 133851895 113939755 0.8512375189010212 2.0748139468048996 chr13 115169878 88001710 0.7641035271392751 1.761085536783615 chr14 107349540 86972827 0.810183508937253 1.9327269069157411 chr15 102531392 75260216 0.7340212059151601 1.7777876753680009 chr16 90354753 89858670 0.9945096081442445 13.6224514226899 chr17 81195210 70553900 0.8689416530852004 15.393672138103286 chr18 78077248 109957771 1.4083202702021465 12.30751819463938 chr19 59128983 37741334 0.638288231678194 7.184919865404644 chr20 63025520 74504500 1.182132253728331 3.6321938102614593 chr21 48129895 26750523 0.5557984907301377 4.2801571371058795 chr22 51304566 16684219 0.32519949588892344 1.1579968727105998 chrMT 16571 5666363 341.9445416691811 174.4757192354956 chrX 155270560 87526864 0.5637054699873563 2.752581042575853 chrY 59373566 5207290 0.08770384450211395 8.875836426338607