BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046540.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,251,334 number of mapped reads = 6,054,407 (96.85%) number of supplementary alignments = 52,313 (0.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,099,235 number of mapped paired reads (second in pair) = 2,955,172 number of mapped paired reads (both in pair) = 5,885,220 number of mapped paired reads (singletons) = 169,187 number of mapped bases = 573,319,040 bp number of sequenced bases = 573,155,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,661,794 duplication rate = 29.32% >>>>>>> Insert size mean insert size = 45,576.0519 std insert size = 2,093,199.452 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 51.0502 >>>>>>> ACTG content number of A's = 169,172,526 bp (29.52%) number of C's = 117,761,750 bp (20.55%) number of T's = 168,647,000 bp (29.42%) number of G's = 117,525,119 bp (20.5%) number of N's = 48,711 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,607,713 number of insertions = 54,184 mapped reads with insertion percentage = 0.88% number of deletions = 55,645 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.1852X std coverageData = 40.6261X There is a 1.77% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.02% 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 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 76841311 0.30828934624800797 40.398730673944954 chr2 243199373 119479271 0.49128116378819775 74.3842382718194 chr3 198022430 64555964 0.3260032916473149 55.30072549267116 chr4 191154276 13619836 0.0712504908862201 6.001564435916502 chr5 180915260 16810687 0.09292022685095773 9.049139884012668 chr6 171115067 9836506 0.05748474504585853 3.2863692010196215 chr7 159138663 21166280 0.13300526472313018 13.102174536955237 chr8 146364022 95807542 0.6545839659967803 123.39313932825254 chr9 141213431 16930945 0.11989613792472757 18.996639499042352 chr10 135534747 23031040 0.16992719955422206 31.356110953933964 chr11 135006516 6735551 0.049890562319229094 1.536343550240683 chr12 133851895 13071266 0.09765469513898178 10.856201981769283 chr13 115169878 14397358 0.1250097529841961 18.754377380978752 chr14 107349540 4641942 0.04324137765285254 0.9203981131575875 chr15 102531392 5380024 0.05247196878005909 3.836000905205378 chr16 90354753 7195657 0.0796378359863371 8.524444236669241 chr17 81195210 37308734 0.4594942731227618 46.809351520404455 chr18 78077248 3737287 0.04786653084903812 2.7634414150493667 chr19 59128983 3359137 0.056810329377726655 0.8513068574178073 chr20 63025520 3379459 0.05362048579686451 1.7349238818291468 chr21 48129895 1298008 0.026968851687708854 0.9086239438647513 chr22 51304566 1563991 0.030484440702607248 3.2397333133293245 chrMT 16571 226194 13.64999094804176 6.370294797467778 chrX 155270560 12655071 0.08150335131141409 16.75590365142305 chrY 59373566 289979 0.0048839747978081695 0.2882890846824443