BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124867.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 = 3,838,788 number of mapped reads = 3,807,348 (99.18%) number of supplementary alignments = 13,188 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,906,306 number of mapped paired reads (second in pair) = 1,901,042 number of mapped paired reads (both in pair) = 3,797,240 number of mapped paired reads (singletons) = 10,108 number of mapped bases = 330,145,778 bp number of sequenced bases = 329,982,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,880 duplication rate = 4.35% >>>>>>> Insert size mean insert size = 24,072.7982 std insert size = 1,458,399.5883 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.9338 >>>>>>> ACTG content number of A's = 92,093,873 bp (27.91%) number of C's = 61,972,445 bp (18.78%) number of T's = 97,165,540 bp (29.45%) number of G's = 78,625,799 bp (23.83%) number of N's = 124,626 bp (0.04%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,189,831 number of insertions = 40,265 mapped reads with insertion percentage = 1.03% number of deletions = 99,450 mapped reads with deletion percentage = 2.56% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.1066X std coverageData = 0.7256X There is a 7.89% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 25382542 0.10183542130472766 0.9430653066353011 chr2 243199373 30595853 0.1258056409545102 0.8660219073427657 chr3 198022430 21578292 0.10896892841886649 0.4034747097972204 chr4 191154276 15159210 0.07930353595647528 0.4592535051730531 chr5 180915260 17333906 0.09581229355666293 0.3788352265970919 chr6 171115067 19038674 0.1112624056653059 0.6961748557403039 chr7 159138663 18200798 0.11437068564538587 1.014442967146837 chr8 146364022 20442742 0.13967054007302424 0.6489491944663213 chr9 141213431 12887927 0.0912655893191916 0.807880938417267 chr10 135534747 16737559 0.1234927527477511 1.1796209774511541 chr11 135006516 15652280 0.11593721891171534 0.7206478696057017 chr12 133851895 21383288 0.15975334529257132 0.5216916074222744 chr13 115169878 5872530 0.050990155603012795 0.26800712697229245 chr14 107349540 9401989 0.08758294632655156 0.3752470992112157 chr15 102531392 6877828 0.06708021675937063 0.318395038550583 chr16 90354753 9342122 0.10339380818184518 0.5880221973520693 chr17 81195210 17284105 0.21287099325194184 1.5739350021248704 chr18 78077248 5976361 0.07654420657859252 0.8719201646682292 chr19 59128983 7279996 0.1231206022941406 0.5996319364647033 chr20 63025520 7232662 0.11475767276493712 0.42688743704593934 chr21 48129895 3847838 0.07994694357841421 0.3997881871484805 chr22 51304566 5179914 0.10096399607005739 0.41105397199545074 chrMT 16571 116742 7.0449580592601535 5.4966484539515115 chrX 155270560 16738990 0.107805304495585 0.47310125675175385 chrY 59373566 601630 0.010132960516469568 0.5480291214917522