BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472605.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 = 17,217,818 number of mapped reads = 17,104,873 (99.34%) number of supplementary alignments = 79,416 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,569,520 number of mapped paired reads (second in pair) = 8,535,353 number of mapped paired reads (both in pair) = 17,035,664 number of mapped paired reads (singletons) = 69,209 number of mapped bases = 1,678,300,557 bp number of sequenced bases = 1,678,033,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,045,692 duplication rate = 49.95% >>>>>>> Insert size mean insert size = 18,952.2399 std insert size = 1,373,256.372 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 55.1091 >>>>>>> ACTG content number of A's = 450,598,575 bp (26.85%) number of C's = 390,526,111 bp (23.27%) number of T's = 449,842,222 bp (26.81%) number of G's = 386,742,035 bp (23.05%) number of N's = 324,601 bp (0.02%) GC percentage = 46.32% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,458,261 number of insertions = 102,419 mapped reads with insertion percentage = 0.59% number of deletions = 86,585 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.5421X std coverageData = 25.7513X There is a 3.47% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 249458047 1.000832198528404 40.31431129207567 chr2 243199373 137426795 0.5650787389159921 24.938515035751053 chr3 198022430 137412091 0.6939218501661655 19.417097112016908 chr4 191154276 35094937 0.18359483101492324 8.900080465733394 chr5 180915260 74966767 0.4143750339247225 14.705655010326145 chr6 171115067 155421591 0.9082870008168247 31.945309019381497 chr7 159138663 109270235 0.6866353715690071 25.70438950672582 chr8 146364022 105089540 0.7180011765459684 29.6123193830325 chr9 141213431 57926044 0.4102020862307354 16.23861372734521 chr10 135534747 38273525 0.28238902456504383 13.146020673984602 chr11 135006516 59660601 0.44190904830104644 17.965539636220722 chr12 133851895 101000075 0.7545658953875849 31.874223580168433 chr13 115169878 16161687 0.14032911452767188 5.561844539797729 chr14 107349540 46650944 0.43457050677627496 17.051030013391745 chr15 102531392 50423807 0.4917889635205577 62.920294785055404 chr16 90354753 69255000 0.7664787706298085 26.821060026474232 chr17 81195210 93100165 1.1466213955232087 38.920977324342566 chr18 78077248 14109820 0.18071615433986607 9.364622594742206 chr19 59128983 20928146 0.3539405709041199 9.07383203784701 chr20 63025520 30916226 0.49053504040902796 18.481737056993317 chr21 48129895 9239421 0.19196844289811976 15.399801943449624 chr22 51304566 18360944 0.35788128487433263 13.171810287677095 chrMT 16571 2376 0.1433830185263412 0.46280531583309475 chrX 155270560 44227849 0.2848437527371576 15.09870148930617 chrY 59373566 3923924 0.06608873719998559 4.793288269524833