BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038453.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 = 16,842,540 number of mapped reads = 15,939,433 (94.64%) number of supplementary alignments = 260,705 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,101,523 number of mapped paired reads (second in pair) = 7,837,910 number of mapped paired reads (both in pair) = 15,630,582 number of mapped paired reads (singletons) = 308,851 number of mapped bases = 2,149,629,184 bp number of sequenced bases = 2,148,163,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,674,518 duplication rate = 11.72% >>>>>>> Insert size mean insert size = 96,421.6218 std insert size = 3,024,131.0068 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.3867 >>>>>>> ACTG content number of A's = 614,515,145 bp (28.61%) number of C's = 425,299,836 bp (19.8%) number of T's = 627,316,169 bp (29.2%) number of G's = 480,862,421 bp (22.38%) number of N's = 170,081 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 27,898,177 number of insertions = 374,046 mapped reads with insertion percentage = 2.22% number of deletions = 714,211 mapped reads with deletion percentage = 4.31% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.6944X std coverageData = 9.3751X There is a 30.18% of reference with a coverageData >= 1X There is a 15.87% of reference with a coverageData >= 2X There is a 8.16% of reference with a coverageData >= 3X There is a 4.6% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 1.52% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 186411871 0.7478892941253695 12.201966144751692 chr2 243199373 193861347 0.7971293042766192 10.313391726357631 chr3 198022430 148650219 0.7506736433847419 1.6291446524042794 chr4 191154276 93495130 0.48910823213810817 9.24955738254125 chr5 180915260 149156712 0.8244562233169275 1.5681501407986913 chr6 171115067 125995302 0.7363191576811877 6.762674995308335 chr7 159138663 104709161 0.6579743666691481 9.219421342415753 chr8 146364022 136961640 0.9357602922390312 3.523176651258938 chr9 141213431 92374541 0.6541484074556619 14.491206075641443 chr10 135534747 117901701 0.8699001813903855 26.849358976631226 chr11 135006516 98567971 0.7300978791275526 6.663833202446653 chr12 133851895 89286388 0.6670535968131045 1.5478473250832094 chr13 115169878 73496035 0.6381532765016908 1.328584462847141 chr14 107349540 71119675 0.6625056334661518 1.4489322492480938 chr15 102531392 59233875 0.5777145305898119 1.281131580643283 chr16 90354753 69640082 0.7707406604276811 10.131226763642308 chr17 81195210 53370716 0.657313602612765 10.120306874863394 chr18 78077248 86046293 1.1020661614507725 10.036878532478134 chr19 59128983 29608656 0.5007469179708367 5.162298911061947 chr20 63025520 57690762 0.9153555892914489 3.282338640423372 chr21 48129895 21133526 0.4390935405115677 4.147709624830822 chr22 51304566 12514378 0.24392327965507007 0.8437946061795576 chrMT 16571 1924164 116.11634783658198 63.88660863448052 chrX 155270560 71765115 0.46219396001405544 1.9389317802718102 chrY 59373566 4713924 0.07939432170875503 8.994282664141855