BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927023.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 = 35,718,702 number of mapped reads = 35,194,038 (98.53%) number of supplementary alignments = 321,701 (0.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,645,740 number of mapped paired reads (second in pair) = 17,548,298 number of mapped paired reads (both in pair) = 34,885,034 number of mapped paired reads (singletons) = 309,004 number of mapped bases = 3,323,853,043 bp number of sequenced bases = 3,321,352,709 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,738,394 duplication rate = 5.75% >>>>>>> Insert size mean insert size = 96,245.8413 std insert size = 3,039,352.4688 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.5078 >>>>>>> ACTG content number of A's = 955,057,290 bp (28.76%) number of C's = 659,728,577 bp (19.86%) number of T's = 966,444,833 bp (29.1%) number of G's = 739,404,470 bp (22.26%) number of N's = 717,539 bp (0.02%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 30,506,027 number of insertions = 535,732 mapped reads with insertion percentage = 1.5% number of deletions = 1,755,164 mapped reads with deletion percentage = 4.86% homopolymer indels = 52.99% >>>>>>> Coverage mean coverageData = 1.0737X std coverageData = 5.157X There is a 38.03% of reference with a coverageData >= 1X There is a 22.76% of reference with a coverageData >= 2X There is a 14.18% of reference with a coverageData >= 3X There is a 9.25% of reference with a coverageData >= 4X There is a 6.2% of reference with a coverageData >= 5X There is a 4.24% of reference with a coverageData >= 6X There is a 2.95% of reference with a coverageData >= 7X There is a 2.08% of reference with a coverageData >= 8X There is a 1.48% of reference with a coverageData >= 9X There is a 1.07% of reference with a coverageData >= 10X There is a 0.77% of reference with a coverageData >= 11X There is a 0.57% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 270556519 1.0854798191255057 6.6070591950018835 chr2 243199373 294708043 1.211796064128833 8.181365271210597 chr3 198022430 226650364 1.1445691480505515 2.207460229561795 chr4 191154276 203960856 1.0669960425054787 3.333078719583319 chr5 180915260 200619895 1.108916378861573 2.101461914626301 chr6 171115067 188294804 1.1003987392881072 2.1641118151398224 chr7 159138663 171711296 1.0790042643502666 3.2599616971724523 chr8 146364022 171218530 1.1698129612754151 2.599213574284782 chr9 141213431 142159295 1.0066981164135866 5.951968656851429 chr10 135534747 171469323 1.2651318336839483 13.776068257974865 chr11 135006516 158923472 1.1771540863998002 5.355990757088017 chr12 133851895 146885843 1.0973758944540906 2.118191378540254 chr13 115169878 100116266 0.869292107785336 1.8511580160683874 chr14 107349540 98145366 0.9142597723287869 1.9945251702408509 chr15 102531392 96469460 0.9408773071178045 1.9984679748356948 chr16 90354753 103837417 1.149219200455343 6.703820488384801 chr17 81195210 84901391 1.0456453157766326 2.7212316885506946 chr18 78077248 89847273 1.1507484613187187 5.970518730924349 chr19 59128983 53157055 0.8990016790919607 3.943304781434936 chr20 63025520 76918509 1.2204343415175314 2.4935996223062737 chr21 48129895 42971931 0.8928324277457909 2.946455645266473 chr22 51304566 40814199 0.7955276144427379 1.9547287134825502 chrMT 16571 551938 33.30746484822883 26.787698438976598 chrX 155270560 182981143 1.1784664330443582 2.8297365876240885 chrY 59373566 5982855 0.10076630734963772 3.2802059657463087