BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472401.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,625,970 number of mapped reads = 19,475,637 (99.23%) number of supplementary alignments = 77,279 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,766,967 number of mapped paired reads (second in pair) = 9,708,670 number of mapped paired reads (both in pair) = 19,379,500 number of mapped paired reads (singletons) = 96,137 number of mapped bases = 1,911,874,137 bp number of sequenced bases = 1,911,640,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,697,930 duplication rate = 48.56% >>>>>>> Insert size mean insert size = 17,076.482 std insert size = 1,300,333.0687 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 55.0811 >>>>>>> ACTG content number of A's = 515,206,679 bp (26.95%) number of C's = 441,685,309 bp (23.11%) number of T's = 516,351,995 bp (27.01%) number of G's = 438,154,408 bp (22.92%) number of N's = 242,551 bp (0.01%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 10,303,309 number of insertions = 116,440 mapped reads with insertion percentage = 0.59% number of deletions = 100,108 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.6176X std coverageData = 19.9739X There is a 5.03% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 239437559 0.9606297390127666 26.897853575172135 chr2 243199373 133080340 0.5472067561621551 17.083278534794715 chr3 198022430 162986599 0.8230714015578943 19.30463619275185 chr4 191154276 59971628 0.31373416935752985 11.446087429636481 chr5 180915260 104616014 0.5782597554236165 16.95639137855144 chr6 171115067 143036753 0.8359097507176267 20.09081540693659 chr7 159138663 126491606 0.7948515063243934 25.906521500439887 chr8 146364022 98148642 0.6705790170209999 18.113996861626894 chr9 141213431 79932879 0.5660430345326005 13.986759164084496 chr10 135534747 52056992 0.38408594956096387 13.769021133254354 chr11 135006516 64921825 0.4808791969715002 13.785307964793967 chr12 133851895 88001235 0.6574522908323412 19.32183681802128 chr13 115169878 42870728 0.3722390675798059 13.46817149458392 chr14 107349540 33948781 0.3162452396163039 10.81942055461778 chr15 102531392 50264940 0.4902395161083934 17.99209892230027 chr16 90354753 109316887 1.2098631601593774 36.38603100725973 chr17 81195210 54474050 0.6709022613526093 13.745691115079888 chr18 78077248 26809132 0.3433667641564416 11.596539548249526 chr19 59128983 65133148 1.101543518852675 46.832544184919186 chr20 63025520 37753381 0.5990173662986041 19.38182153360002 chr21 48129895 18744802 0.38946276529379503 20.821712362374342 chr22 51304566 46240153 0.9012872850342404 32.24791138399742 chrMT 16571 7358 0.4440287248808159 0.8405786646917703 chrX 155270560 71524976 0.46064737578070175 16.024472395229253 chrY 59373566 2103729 0.03543208100385953 2.1960362855639275