BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,758,952 number of mapped reads = 28,279,308 (98.33%) number of supplementary alignments = 525,131 (1.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,196,840 number of mapped paired reads (second in pair) = 14,082,468 number of mapped paired reads (both in pair) = 28,039,358 number of mapped paired reads (singletons) = 239,950 number of mapped bases = 2,646,268,372 bp number of sequenced bases = 2,644,258,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,306,165 duplication rate = 6.38% >>>>>>> Insert size mean insert size = 170,755.0521 std insert size = 4,087,626.3051 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.1841 >>>>>>> ACTG content number of A's = 743,646,467 bp (28.12%) number of C's = 541,321,045 bp (20.47%) number of T's = 753,119,914 bp (28.48%) number of G's = 605,980,641 bp (22.92%) number of N's = 190,858 bp (0.01%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 24,851,147 number of insertions = 439,811 mapped reads with insertion percentage = 1.53% number of deletions = 1,385,361 mapped reads with deletion percentage = 4.77% homopolymer indels = 52.2% >>>>>>> Coverage mean coverageData = 0.8548X std coverageData = 3.3043X There is a 32.22% of reference with a coverageData >= 1X There is a 18.68% of reference with a coverageData >= 2X There is a 10.97% of reference with a coverageData >= 3X There is a 6.93% of reference with a coverageData >= 4X There is a 4.51% of reference with a coverageData >= 5X There is a 3.03% of reference with a coverageData >= 6X There is a 2.08% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.05% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.42% 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 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% 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 0.02% of reference with a coverageData >= 26X There is a 0.02% 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 0.01% 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 223400496 0.8962886234895279 3.863882020532606 chr2 243199373 233385538 0.9596469559977032 5.173044284798103 chr3 198022430 170157700 0.8592849809993747 1.8331087363687817 chr4 191154276 144010854 0.75337500689757 2.5886683545309244 chr5 180915260 151104281 0.8352213130058791 1.7913332228221643 chr6 171115067 145429735 0.8498943871494379 2.2226734020595855 chr7 159138663 129577250 0.814241162752511 2.575964633140077 chr8 146364022 123284528 0.8423144316162615 2.1058588687582502 chr9 141213431 111811331 0.7917896350808161 3.787394066410611 chr10 135534747 126463057 0.9330674221865778 4.675104508890879 chr11 135006516 123675716 0.91607219906334 3.8570935625309395 chr12 133851895 119528611 0.8929915486067642 2.082538712797866 chr13 115169878 78434767 0.6810354266416779 1.6417951818983563 chr14 107349540 76529163 0.7128969812073718 1.7544556764812793 chr15 102531392 87753352 0.8558681423148922 1.9960239785292895 chr16 90354753 93352747 1.0331802578221867 4.182403468566769 chr17 81195210 84612918 1.0420924830417952 2.5945752926631833 chr18 78077248 65928869 0.8444056455473431 3.966382782528549 chr19 59128983 55940901 0.9460825835614322 2.796757402744581 chr20 63025520 69434323 1.1016858409101582 2.335365902340189 chr21 48129895 35437020 0.7362787722682544 3.541092226753158 chr22 51304566 47546015 0.9267404191665903 2.3047139775910663 chrMT 16571 6274377 378.63599058596344 281.9790976614372 chrX 155270560 138204184 0.8900862082290423 2.207764924288957 chrY 59373566 4990639 0.08405489742691218 2.367842834451276