BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926916.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 = 33,525,776 number of mapped reads = 29,986,594 (89.44%) number of supplementary alignments = 441,698 (1.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,051,651 number of mapped paired reads (second in pair) = 14,934,943 number of mapped paired reads (both in pair) = 29,572,200 number of mapped paired reads (singletons) = 414,394 number of mapped bases = 2,761,978,394 bp number of sequenced bases = 2,759,928,775 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,420,349 duplication rate = 6.46% >>>>>>> Insert size mean insert size = 166,286.4112 std insert size = 4,044,763.4481 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.9696 >>>>>>> ACTG content number of A's = 775,331,210 bp (28.09%) number of C's = 554,893,470 bp (20.11%) number of T's = 784,076,448 bp (28.41%) number of G's = 645,378,637 bp (23.38%) number of N's = 249,010 bp (0.01%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 27,993,661 number of insertions = 439,722 mapped reads with insertion percentage = 1.44% number of deletions = 1,427,444 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.39% >>>>>>> Coverage mean coverageData = 0.8922X std coverageData = 3.0052X There is a 34.6% of reference with a coverageData >= 1X There is a 19.4% of reference with a coverageData >= 2X There is a 11.4% of reference with a coverageData >= 3X There is a 7.19% of reference with a coverageData >= 4X There is a 4.69% of reference with a coverageData >= 5X There is a 3.16% of reference with a coverageData >= 6X There is a 2.17% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 231789205 0.929944343047394 2.749056941322608 chr2 243199373 236675066 0.9731730106064048 4.099616338266644 chr3 198022430 185836402 0.9384613753098576 1.917380578180711 chr4 191154276 161083548 0.8426886982114907 2.075006194995992 chr5 180915260 166973187 0.9229358927489035 1.8694931793215088 chr6 171115067 157808783 0.9222378003685672 2.155302678848242 chr7 159138663 138062075 0.8675583443854873 1.9967456996291768 chr8 146364022 141654309 0.9678219214282046 2.0626425928995147 chr9 141213431 115647585 0.818955988683541 2.799475157400299 chr10 135534747 138450325 1.021511664459004 8.525697416406613 chr11 135006516 133483385 0.9887180926882078 2.286106033483316 chr12 133851895 125300271 0.9361112967433147 1.964478095756543 chr13 115169878 80793545 0.7015162853606566 1.6134508089876327 chr14 107349540 83857114 0.7811595093933332 1.7648012291025887 chr15 102531392 82592547 0.8055342406743098 1.8569638021348531 chr16 90354753 89893887 0.9948993718127922 4.2552798503665015 chr17 81195210 74561458 0.9182987272278746 2.13856807164278 chr18 78077248 71155054 0.9113417265936422 2.925942664910317 chr19 59128983 48198491 0.8151415524938084 2.134879961507192 chr20 63025520 67418453 1.0697008608576335 2.148109824532913 chr21 48129895 34256593 0.7117529136516919 2.6367008663596443 chr22 51304566 37102125 0.7231739373840527 1.8520171313714615 chrMT 16571 23516 1.4191056665258583 1.825299413560935 chrX 155270560 155231028 0.9997453992566266 2.031187718322878 chrY 59373566 4130442 0.06956701910072237 1.49759598823574