BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124968.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 = 5,944,054 number of mapped reads = 5,866,103 (98.69%) number of supplementary alignments = 54,206 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,939,143 number of mapped paired reads (second in pair) = 2,926,960 number of mapped paired reads (both in pair) = 5,839,354 number of mapped paired reads (singletons) = 26,749 number of mapped bases = 497,041,452 bp number of sequenced bases = 496,747,370 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 681,946 duplication rate = 8.39% >>>>>>> Insert size mean insert size = 74,907.2737 std insert size = 2,568,674.533 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.4462 >>>>>>> ACTG content number of A's = 143,601,689 bp (28.91%) number of C's = 90,202,452 bp (18.16%) number of T's = 150,898,544 bp (30.38%) number of G's = 112,039,621 bp (22.55%) number of N's = 5,064 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 3,655,704 number of insertions = 76,713 mapped reads with insertion percentage = 1.27% number of deletions = 158,663 mapped reads with deletion percentage = 2.65% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.1606X std coverageData = 1.9675X There is a 10.51% of reference with a coverageData >= 1X There is a 3.2% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 40636756 0.16303572619784967 1.426897828500849 chr2 243199373 43610947 0.17932179043899096 2.1638905749063064 chr3 198022430 34684502 0.17515441053824055 0.626844198692277 chr4 191154276 29389848 0.1537493621120984 1.5387387889040989 chr5 180915260 29375660 0.162372483117234 0.5733543758195703 chr6 171115067 29641152 0.17322350696329972 0.8793022783838513 chr7 159138663 31375430 0.19715780821911266 1.482300090562214 chr8 146364022 30388997 0.20762614052789558 0.7922710469441414 chr9 141213431 19723469 0.1396713390527279 1.6671832158844846 chr10 135534747 27000281 0.19921298115530478 6.877126404050581 chr11 135006516 19668082 0.14568246468933396 0.8450501518457124 chr12 133851895 23310816 0.17415379886851806 0.5682234788720514 chr13 115169878 12670114 0.11001239403935116 0.43660736503887676 chr14 107349540 17123574 0.15951231835739585 0.6301137069183045 chr15 102531392 14005204 0.13659430274778675 0.5234566627388824 chr16 90354753 17074573 0.1889726044627669 3.224527185855945 chr17 81195210 10980350 0.13523396269311946 1.2891051956261455 chr18 78077248 10210234 0.13077092573754648 1.815246053985348 chr19 59128983 6962437 0.11774998734546137 0.9463369798102493 chr20 63025520 10461227 0.16598398553474847 0.7049594090703701 chr21 48129895 5515903 0.11460450931796132 0.8878620053130493 chr22 51304566 4173713 0.08135168709935096 0.447629739687577 chrMT 16571 120391 7.265162030052501 5.115971366910132 chrX 155270560 20794341 0.13392326916319489 0.6770400151820877 chrY 59373566 8143451 0.13715617148547218 3.1791255467025428