BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472380.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 = 19,158,804 number of mapped reads = 19,008,804 (99.22%) number of supplementary alignments = 66,757 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,528,002 number of mapped paired reads (second in pair) = 9,480,802 number of mapped paired reads (both in pair) = 18,918,506 number of mapped paired reads (singletons) = 90,298 number of mapped bases = 1,864,293,090 bp number of sequenced bases = 1,864,083,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,018,096 duplication rate = 47.37% >>>>>>> Insert size mean insert size = 15,835.6179 std insert size = 1,238,181.2003 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 54.9098 >>>>>>> ACTG content number of A's = 498,255,905 bp (26.73%) number of C's = 435,260,991 bp (23.35%) number of T's = 499,138,095 bp (26.78%) number of G's = 431,197,956 bp (23.13%) number of N's = 230,723 bp (0.01%) GC percentage = 46.48% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 10,054,298 number of insertions = 104,680 mapped reads with insertion percentage = 0.54% number of deletions = 87,742 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.6022X std coverageData = 18.395X There is a 5.15% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% 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 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167204015 0.670826874288911 19.500966499177515 chr2 243199373 147634394 0.6070508824872669 17.427954443346646 chr3 198022430 135456198 0.6840447216004772 19.629192422579585 chr4 191154276 73369349 0.38382269303774297 16.49933833848351 chr5 180915260 62590997 0.3459685877244407 10.91304204137324 chr6 171115067 149572502 0.8741048034069379 23.34569980819699 chr7 159138663 133738766 0.840391413870305 22.361993960288256 chr8 146364022 83279639 0.5689898231957577 20.77927691757272 chr9 141213431 65502969 0.4638579243924751 14.866213664188109 chr10 135534747 53312055 0.3933460325122384 11.46231186194019 chr11 135006516 53869290 0.3990125187735383 14.56833213862542 chr12 133851895 113166439 0.8454601184391151 21.894163553025184 chr13 115169878 87302348 0.7580310886497597 25.223167100831485 chr14 107349540 37466738 0.34901628828591164 12.129245689346362 chr15 102531392 37389489 0.3646638192525466 13.088486490690984 chr16 90354753 100703898 1.1145390215388005 31.456869616021798 chr17 81195210 62473996 0.7694295759565127 14.990100785939932 chr18 78077248 23459449 0.3004645988547137 11.173615262175657 chr19 59128983 53886494 0.9113380827131764 20.953752188346282 chr20 63025520 50725314 0.8048376911447934 19.94723200083089 chr21 48129895 13802951 0.2867853960620525 12.258685442282834 chr22 51304566 23871071 0.4652816086583795 15.53643688326178 chrMT 16571 23307 1.406493271377708 1.4557972049062868 chrX 155270560 133985374 0.8629155069705423 19.028993991250584 chrY 59373566 506048 0.008523119531004757 0.6583131387445799