BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926924.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 = 14,355,846 number of mapped reads = 13,981,932 (97.4%) number of supplementary alignments = 522,456 (3.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,977,785 number of mapped paired reads (second in pair) = 7,004,147 number of mapped paired reads (both in pair) = 13,774,686 number of mapped paired reads (singletons) = 207,246 number of mapped bases = 1,261,350,519 bp number of sequenced bases = 1,260,399,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 975,861 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 343,224.4298 std insert size = 5,621,432.7385 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.6088 >>>>>>> ACTG content number of A's = 358,238,900 bp (28.42%) number of C's = 246,328,061 bp (19.54%) number of T's = 364,659,238 bp (28.93%) number of G's = 291,122,928 bp (23.1%) number of N's = 49,924 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 12,105,951 number of insertions = 216,320 mapped reads with insertion percentage = 1.52% number of deletions = 646,010 mapped reads with deletion percentage = 4.5% homopolymer indels = 51.45% >>>>>>> Coverage mean coverageData = 0.4075X std coverageData = 1.6757X There is a 22.29% of reference with a coverageData >= 1X There is a 9.35% of reference with a coverageData >= 2X There is a 3.98% of reference with a coverageData >= 3X There is a 1.94% of reference with a coverageData >= 4X There is a 1% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 66767025 0.2678710477515721 1.6865788114142974 chr2 243199373 115579754 0.4752469242591345 2.799449533530779 chr3 198022430 90455603 0.45679473279870364 1.0566129422384767 chr4 191154276 78002723 0.4080616172038966 1.833571844573391 chr5 180915260 74961131 0.41434388121820126 0.9926058866052145 chr6 171115067 73903356 0.43189274501467484 1.4892260218081925 chr7 159138663 66793916 0.419721485281047 1.4666517355180781 chr8 146364022 65085607 0.44468309978527376 1.189064156802326 chr9 141213431 55651981 0.3940983559842831 2.0154338693217078 chr10 135534747 60261559 0.44462073626034804 2.884225587963769 chr11 135006516 64388962 0.47693225414394075 1.5054553175482432 chr12 133851895 62785056 0.4690636318596759 1.146261057964895 chr13 115169878 36311316 0.3152848351545532 0.85818394330184 chr14 107349540 40057078 0.3731462472964486 0.9799134951519719 chr15 102531392 39652831 0.38673844396845797 1.0073473284224395 chr16 90354753 39866351 0.4412202975088649 2.2327125468339326 chr17 81195210 31651909 0.3898248307997479 1.2190430196043502 chr18 78077248 32299027 0.4136803976492614 2.0109315580112095 chr19 59128983 24340558 0.4116518966680012 1.432775365817286 chr20 63025520 32310318 0.5126545247068172 1.2874612569397528 chr21 48129895 15563527 0.32336507278896 1.3326202199250812 chr22 51304566 16354336 0.3187696003509707 0.9503652767580953 chrMT 16571 184128 11.111459779132218 7.499053057463457 chrX 155270560 75148678 0.48398536077927456 1.1891321961638608 chrY 59373566 2973789 0.05008607702626452 1.5662372158808953