BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926977.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 = 21,767,278 number of mapped reads = 21,462,613 (98.6%) number of supplementary alignments = 164,984 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,777,624 number of mapped paired reads (second in pair) = 10,684,989 number of mapped paired reads (both in pair) = 21,275,452 number of mapped paired reads (singletons) = 187,161 number of mapped bases = 2,054,525,024 bp number of sequenced bases = 2,052,968,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,229,226 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 73,335.1476 std insert size = 2,654,840.2452 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.6527 >>>>>>> ACTG content number of A's = 583,898,893 bp (28.44%) number of C's = 420,369,305 bp (20.48%) number of T's = 590,811,481 bp (28.78%) number of G's = 457,721,782 bp (22.3%) number of N's = 167,084 bp (0.01%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 19,386,141 number of insertions = 331,024 mapped reads with insertion percentage = 1.52% number of deletions = 1,099,617 mapped reads with deletion percentage = 4.99% homopolymer indels = 52.92% >>>>>>> Coverage mean coverageData = 0.6637X std coverageData = 2.772X There is a 27.93% of reference with a coverageData >= 1X There is a 15.15% of reference with a coverageData >= 2X There is a 8.37% of reference with a coverageData >= 3X There is a 4.97% of reference with a coverageData >= 4X There is a 3.05% of reference with a coverageData >= 5X There is a 1.92% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 0.82% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% 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 172211111 0.6909154741885277 3.5723503756231216 chr2 243199373 170187828 0.6997872811127683 4.489246005552668 chr3 198022430 139143895 0.7026673443003402 1.5411287976855934 chr4 191154276 110001065 0.5754569937007321 2.189055753725391 chr5 180915260 129214138 0.7142246486006764 1.539927210119783 chr6 171115067 122879815 0.7181121870466264 2.007985897219007 chr7 159138663 109942706 0.6908610637252872 2.26575357757633 chr8 146364022 100294996 0.6852435088180345 1.7911734052690897 chr9 141213431 87767781 0.6215257315007098 3.3881543282537216 chr10 135534747 98526506 0.7269464707821383 4.570437472766066 chr11 135006516 103417853 0.7660211970805912 3.8895764877437675 chr12 133851895 95896131 0.7164346160358805 1.8064600481795383 chr13 115169878 57142408 0.4961575803701034 1.3382330644807814 chr14 107349540 63485420 0.5913897721406165 1.4750709129759305 chr15 102531392 62666562 0.6111939063501645 1.5430254855249728 chr16 90354753 66661088 0.7377706848470937 3.5430115339483272 chr17 81195210 55563212 0.6843163777764723 2.123917273264668 chr18 78077248 50694364 0.6492847186417227 3.5678035516172493 chr19 59128983 34077195 0.5763196535952597 2.246074808695557 chr20 63025520 50905538 0.807697231216815 1.8153916369769532 chr21 48129895 27489406 0.5711503422145425 2.311315756528035 chr22 51304566 24478362 0.4771185862872322 1.397013598311103 chrMT 16571 45872 2.7682095226600687 2.956137536388979 chrX 155270560 118247443 0.7615573937519128 2.09446063877749 chrY 59373566 3584329 0.06036910432497856 1.9269767591908165