BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926964.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 = 29,991,400 number of mapped reads = 29,293,339 (97.67%) number of supplementary alignments = 737,748 (2.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,706,827 number of mapped paired reads (second in pair) = 14,586,512 number of mapped paired reads (both in pair) = 28,911,844 number of mapped paired reads (singletons) = 381,495 number of mapped bases = 2,748,055,380 bp number of sequenced bases = 2,745,907,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,353,440 duplication rate = 6.3% >>>>>>> Insert size mean insert size = 256,720.652 std insert size = 4,929,722.765 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.1565 >>>>>>> ACTG content number of A's = 796,327,191 bp (29%) number of C's = 537,115,752 bp (19.56%) number of T's = 804,675,523 bp (29.3%) number of G's = 607,597,633 bp (22.13%) number of N's = 191,104 bp (0.01%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 27,017,359 number of insertions = 478,624 mapped reads with insertion percentage = 1.61% number of deletions = 1,495,543 mapped reads with deletion percentage = 4.97% homopolymer indels = 52.65% >>>>>>> Coverage mean coverageData = 0.8877X std coverageData = 3.2139X There is a 33.22% of reference with a coverageData >= 1X There is a 19.25% of reference with a coverageData >= 2X There is a 11.62% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 4.85% of reference with a coverageData >= 5X There is a 3.26% of reference with a coverageData >= 6X There is a 2.23% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.09% of reference with a coverageData >= 9X There is a 0.78% 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 0.3% of reference with a coverageData >= 13X There is a 0.22% 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 0.02% 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 227598327 0.9131304310772409 4.186167708490271 chr2 243199373 238604779 0.9811077062275156 5.14897749317157 chr3 198022430 192639451 0.9728163168182513 1.953818282631778 chr4 191154276 172550267 0.9026754232795713 2.7469618103026323 chr5 180915260 167752779 0.9272450483170961 1.8905979278274412 chr6 171115067 158193439 0.924485738009266 2.431630487344286 chr7 159138663 145159762 0.9121589892960205 2.654961410751118 chr8 146364022 138822725 0.9484757463142137 2.2738371136199658 chr9 141213431 114505839 0.8108707379257714 4.016809242308313 chr10 135534747 132034070 0.9741713687634656 4.1967406791559165 chr11 135006516 128738330 0.9535712335543863 2.9470066492235056 chr12 133851895 120286809 0.8986560033386154 2.0930204649922417 chr13 115169878 84935078 0.7374764953732086 1.7121915078637597 chr14 107349540 82408507 0.7676652084396449 1.7959537455829073 chr15 102531392 80693079 0.7870085193030443 1.8514626354432044 chr16 90354753 82549613 0.913616719200151 4.278308997865984 chr17 81195210 68157482 0.8394273750877669 3.2691075726897725 chr18 78077248 74209864 0.9504672090901565 4.64741803033196 chr19 59128983 41270954 0.6979818002281555 2.5791160824097736 chr20 63025520 62127876 0.9857574519020231 2.1828071067602997 chr21 48129895 33515311 0.6963512178865131 2.4371467727093608 chr22 51304566 32410646 0.6317302440488435 1.712577730287003 chrMT 16571 3930654 237.20077243376983 155.45948748593946 chrX 155270560 159919555 1.0299412522245042 2.3026411086324474 chrY 59373566 5040184 0.08488935968575645 2.6490593078972213