BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,036,918 number of mapped reads = 5,897,505 (97.69%) number of supplementary alignments = 60,854 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,957,178 number of mapped paired reads (second in pair) = 2,940,327 number of mapped paired reads (both in pair) = 5,859,570 number of mapped paired reads (singletons) = 37,935 number of mapped bases = 501,245,875 bp number of sequenced bases = 500,901,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 887,282 duplication rate = 9.82% >>>>>>> Insert size mean insert size = 96,848.9263 std insert size = 2,935,443.7416 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 52.1671 >>>>>>> ACTG content number of A's = 142,580,507 bp (28.46%) number of C's = 93,073,040 bp (18.58%) number of T's = 150,524,135 bp (30.05%) number of G's = 114,718,092 bp (22.9%) number of N's = 5,235 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 4,157,094 number of insertions = 90,924 mapped reads with insertion percentage = 1.48% number of deletions = 174,342 mapped reads with deletion percentage = 2.88% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.1619X std coverageData = 2.6133X There is a 9.81% of reference with a coverageData >= 1X There is a 3.2% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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 39026717 0.1565762076877634 1.6219202949984886 chr2 243199373 47259716 0.1943249911256967 3.3816551338744554 chr3 198022430 33560725 0.1694794120039836 0.6952773740440462 chr4 191154276 33126106 0.173295134658667 2.2964274675805654 chr5 180915260 29501621 0.16306872620916554 0.6674539217885913 chr6 171115067 29147970 0.17034134112807262 0.9894399551103157 chr7 159138663 27607686 0.17348195265408256 1.4519178157130823 chr8 146364022 24105377 0.16469468842554763 0.7925358003732712 chr9 141213431 21446093 0.15187006539059306 2.2376187830721936 chr10 135534747 30460834 0.2247455702263568 9.03334571219202 chr11 135006516 22330482 0.16540299432658495 1.110410360827176 chr12 133851895 21247414 0.15873823825953304 0.5898928555538879 chr13 115169878 15095305 0.13106990527505813 0.5244824451977959 chr14 107349540 14668894 0.13664608157612973 0.7185549685943761 chr15 102531392 13928365 0.13584488348700074 0.5579663895097337 chr16 90354753 18000680 0.1992222810901824 4.122851499995216 chr17 81195210 12421682 0.15298540394193205 1.6951794534813993 chr18 78077248 13358619 0.17109490078338827 2.439043148309905 chr19 59128983 6949328 0.11752828557866453 1.0137355554912817 chr20 63025520 10523088 0.16696550857493916 0.9091749230138163 chr21 48129895 6454866 0.13411344446107767 1.167725175496254 chr22 51304566 4911283 0.0957279903702918 0.5715706627938419 chrMT 16571 1583284 95.54547100356044 53.16927882311497 chrX 155270560 15337047 0.09877627156107378 0.775325228781314 chrY 59373566 9192693 0.15482804249958643 4.31406753795634