BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714154.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,056,508 number of mapped reads = 411,139 (38.91%) number of supplementary alignments = 18,787 (1.78%) number of secondary alignments = 0 number of mapped bases = 51,008,709 bp number of sequenced bases = 50,184,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,156 duplication rate = 43.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2035 >>>>>>> ACTG content number of A's = 12,710,939 bp (25.33%) number of C's = 8,691,137 bp (17.32%) number of T's = 11,905,137 bp (23.72%) number of G's = 16,876,833 bp (33.63%) number of N's = 725 bp (0%) GC percentage = 50.95% >>>>>>> Mismatches and indels general error rate = 0.0398 number of mismatches = 1,775,737 number of insertions = 56,965 mapped reads with insertion percentage = 12.52% number of deletions = 137,388 mapped reads with deletion percentage = 31.79% homopolymer indels = 31.65% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 10.1111X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 2432183 0.009757981706292319 1.2785891931623323 chr2 243199373 10610230 0.043627702938197954 34.74027469736244 chr3 198022430 3654902 0.018457010147789825 4.526085408913039 chr4 191154276 2075487 0.010857654055303477 1.116947373186259 chr5 180915260 2075939 0.011474648407215621 1.8860732772304427 chr6 171115067 1925732 0.011254017742341766 1.3971193664716655 chr7 159138663 1935068 0.012159634645164764 1.855488495444213 chr8 146364022 2764563 0.018888268867058054 4.433160034900622 chr9 141213431 1766008 0.012505949239346788 2.2577443251398646 chr10 135534747 2600246 0.019185087643982544 3.5387982789684016 chr11 135006516 1936100 0.014340789299384631 1.6812459487914457 chr12 133851895 1574145 0.011760349003650639 2.007132948176696 chr13 115169878 1904164 0.016533524503690104 2.4862350577039067 chr14 107349540 1313011 0.012231174907689404 1.4655012570219588 chr15 102531392 1058721 0.010325822944059903 1.166774488446355 chr16 90354753 1382565 0.01530151933457225 1.894452652592364 chr17 81195210 820530 0.010105645394599017 0.964946068179612 chr18 78077248 1137884 0.01457382309376478 2.7207083203170503 chr19 59128983 646382 0.010931728692171147 1.4038654133891961 chr20 63025520 666462 0.010574478401764873 0.906982896036467 chr21 48129895 345844 0.0071856379491374335 0.8073445753372034 chr22 51304566 311579 0.0060731241737821155 0.6764162630951306 chrMT 16571 1368138 82.56218695311085 665.459826789234 chrX 155270560 4414327 0.02842990326047642 2.210422000073678 chrY 59373566 288499 0.004859047879994272 0.7852993026180827