BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038465.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,834,032 number of mapped reads = 12,486,526 (97.29%) number of supplementary alignments = 117,053 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,306,858 number of mapped paired reads (second in pair) = 6,179,668 number of mapped paired reads (both in pair) = 12,344,994 number of mapped paired reads (singletons) = 141,532 number of mapped bases = 1,835,455,333 bp number of sequenced bases = 1,834,798,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,183,062 duplication rate = 6.99% >>>>>>> Insert size mean insert size = 83,624.1518 std insert size = 2,881,893.6758 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 54.4483 >>>>>>> ACTG content number of A's = 532,069,617 bp (29%) number of C's = 388,856,486 bp (21.19%) number of T's = 526,860,234 bp (28.71%) number of G's = 386,970,707 bp (21.09%) number of N's = 41,528 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 19,769,162 number of insertions = 223,543 mapped reads with insertion percentage = 1.69% number of deletions = 237,899 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.5929X std coverageData = 5.8153X There is a 35.33% of reference with a coverageData >= 1X There is a 14.14% of reference with a coverageData >= 2X There is a 4.66% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 131190095 0.5263380868367024 14.526854703714879 chr2 243199373 175140524 0.7201520375630245 4.85176955935558 chr3 198022430 118374822 0.5977849175974661 0.9833349781984757 chr4 191154276 105266325 0.5506877858175665 4.114580649117167 chr5 180915260 105338903 0.5822554880113485 1.0339399622647463 chr6 171115067 117101854 0.6843456631437371 5.149944982115221 chr7 159138663 125285403 0.7872719340365453 4.687258433762771 chr8 146364022 83827206 0.5727309543324793 4.083942797366023 chr9 141213431 76003688 0.5382185494806085 6.754531069777817 chr10 135534747 76268217 0.5627207685716195 9.281341592630453 chr11 135006516 94818719 0.7023269824991262 3.575053555449298 chr12 133851895 67901897 0.5072912639750076 0.9309343876865354 chr13 115169878 105642654 0.9172767726644635 1.2663205037110223 chr14 107349540 40506013 0.3773282400651181 0.86012419085417 chr15 102531392 39558639 0.3858197789804707 0.7931043242010765 chr16 90354753 62639999 0.6932673370265314 3.930163221279279 chr17 81195210 53519426 0.6591451145948142 3.0146636287830484 chr18 78077248 33786128 0.43272693217875713 7.0109713614913485 chr19 59128983 37872194 0.6405013595447768 6.645920585670973 chr20 63025520 57415003 0.9109802346731927 1.8312609245049125 chr21 48129895 19574663 0.40670487645983855 2.5471528397342835 chr22 51304566 18062385 0.3520619392823633 2.0512840876419487 chrMT 16571 3735405 225.41820047070183 28.358360467193865 chrX 155270560 70895674 0.4565944374773943 1.2248999535206921 chrY 59373566 15729497 0.2649242425492853 5.0481040987298895