BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124891.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 = 4,823,212 number of mapped reads = 4,788,561 (99.28%) number of supplementary alignments = 65,514 (1.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,398,212 number of mapped paired reads (second in pair) = 2,390,349 number of mapped paired reads (both in pair) = 4,777,658 number of mapped paired reads (singletons) = 10,903 number of mapped bases = 680,525,943 bp number of sequenced bases = 680,028,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 755,990 duplication rate = 13.69% >>>>>>> Insert size mean insert size = 40,976.1339 std insert size = 1,894,561.2817 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 53.6025 >>>>>>> ACTG content number of A's = 203,882,522 bp (29.98%) number of C's = 134,929,165 bp (19.84%) number of T's = 202,377,544 bp (29.76%) number of G's = 138,799,733 bp (20.41%) number of N's = 40,020 bp (0.01%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 7,548,805 number of insertions = 123,780 mapped reads with insertion percentage = 2.47% number of deletions = 278,951 mapped reads with deletion percentage = 5.61% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 0.2198X std coverageData = 2.7968X There is a 10.25% of reference with a coverageData >= 1X There is a 6.68% of reference with a coverageData >= 2X There is a 1.95% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.1% 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 0.02% 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% 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 53568382 0.21491774738647493 4.215110823092589 chr2 243199373 57259601 0.23544304532396965 2.556855978167087 chr3 198022430 40173493 0.20287344721504527 0.7818469537893485 chr4 191154276 60240696 0.3151417653874507 2.001738577433636 chr5 180915260 48619577 0.2687422664069355 0.8201456710747752 chr6 171115067 31224849 0.18247866507278404 1.9792152704906363 chr7 159138663 33919397 0.21314365950152542 2.555457251577359 chr8 146364022 34803219 0.23778534181029817 1.2233828630473542 chr9 141213431 37001472 0.2620251610485974 4.841910581700385 chr10 135534747 33317571 0.2458230950916225 6.759114910657606 chr11 135006516 32627489 0.24167343893238458 2.2017731450961273 chr12 133851895 27448089 0.20506313339829818 0.716378867041326 chr13 115169878 13043642 0.11325567263342938 0.5063828555946805 chr14 107349540 22346715 0.20816777603332068 0.7508268098499052 chr15 102531392 28554403 0.27849424886380164 0.864492185855234 chr16 90354753 22664815 0.2508425317702988 4.11205284019203 chr17 81195210 11570394 0.14250094309750538 3.49587258382064 chr18 78077248 12411636 0.1589661049528795 4.084731623279871 chr19 59128983 6471867 0.10945337923366617 2.3541036164123 chr20 63025520 12773833 0.2026771536355432 0.9598468177457842 chr21 48129895 9123018 0.18954992525955022 1.1753850109922341 chr22 51304566 4184970 0.08157110226797358 0.44584598008197823 chrMT 16571 25891 1.562428338663931 1.8586349800648108 chrX 155270560 45454140 0.29274152163810063 1.4115666196896226 chrY 59373566 1696784 0.028578104943199806 2.1014037413196363