BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472510.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 = 16,291,552 number of mapped reads = 16,054,961 (98.55%) number of supplementary alignments = 69,238 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,062,422 number of mapped paired reads (second in pair) = 7,992,539 number of mapped paired reads (both in pair) = 15,929,922 number of mapped paired reads (singletons) = 125,039 number of mapped bases = 1,580,696,699 bp number of sequenced bases = 1,580,499,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,453,581 duplication rate = 44.58% >>>>>>> Insert size mean insert size = 32,090.9494 std insert size = 1,826,662.676 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 54.8881 >>>>>>> ACTG content number of A's = 444,430,143 bp (28.12%) number of C's = 348,386,733 bp (22.04%) number of T's = 440,599,768 bp (27.88%) number of G's = 346,839,948 bp (21.94%) number of N's = 243,298 bp (0.02%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,009,290 number of insertions = 97,153 mapped reads with insertion percentage = 0.6% number of deletions = 83,421 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.5106X std coverageData = 21.9401X There is a 5.11% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% 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 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 140192822 0.5624572626440919 20.42344016936546 chr2 243199373 150675537 0.6195556145615556 24.57374369268752 chr3 198022430 214046248 1.0809192069807445 33.080194724830335 chr4 191154276 76404247 0.39969938731582444 16.362323853776818 chr5 180915260 107941795 0.5966428426214572 22.064953622016056 chr6 171115067 36339882 0.21237102399638486 7.874901112221684 chr7 159138663 32279987 0.20284188890037363 7.4501719743911075 chr8 146364022 65027086 0.44428326791948913 26.020621834373426 chr9 141213431 128149907 0.9074909241458767 29.348426552246437 chr10 135534747 28860892 0.21294090732319734 9.382254885751326 chr11 135006516 65273280 0.48348244169192545 20.845657108052464 chr12 133851895 50442062 0.37684981598504824 17.41474321606217 chr13 115169878 36391735 0.3159830993308858 13.377458843269372 chr14 107349540 36005125 0.33540083171292584 11.756758765005339 chr15 102531392 70943815 0.6919228698270282 35.53120442990271 chr16 90354753 63405808 0.7017429177190048 25.277311122232433 chr17 81195210 47475591 0.5847092580953975 16.097053433071473 chr18 78077248 32190709 0.41229307928476167 21.09392232509583 chr19 59128983 49860853 0.8432557177585821 48.68309319380468 chr20 63025520 23298358 0.36966546249836574 23.210010277820647 chr21 48129895 7591868 0.1577370571865989 7.670316073555061 chr22 51304566 16074716 0.31331940318918206 8.877078688444685 chrMT 16571 5383 0.3248446080502082 0.8703960202326301 chrX 155270560 99874494 0.6432287872214797 21.589458851904002 chrY 59373566 1944499 0.03275024781230085 1.247981003721178