BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124834.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 = 26,097,260 number of mapped reads = 25,826,586 (98.96%) number of supplementary alignments = 98,799 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,940,452 number of mapped paired reads (second in pair) = 12,886,134 number of mapped paired reads (both in pair) = 25,723,776 number of mapped paired reads (singletons) = 102,810 number of mapped bases = 2,250,083,305 bp number of sequenced bases = 2,248,949,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,591,456 duplication rate = 9.2% >>>>>>> Insert size mean insert size = 30,690.7015 std insert size = 1,634,792.2744 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.7719 >>>>>>> ACTG content number of A's = 635,385,013 bp (28.25%) number of C's = 418,229,485 bp (18.6%) number of T's = 673,124,327 bp (29.93%) number of G's = 522,189,676 bp (23.22%) number of N's = 20,932 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 16,570,256 number of insertions = 280,563 mapped reads with insertion percentage = 1.07% number of deletions = 709,537 mapped reads with deletion percentage = 2.7% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.7268X std coverageData = 6.4877X There is a 32.59% of reference with a coverageData >= 1X There is a 16.24% of reference with a coverageData >= 2X There is a 8.47% of reference with a coverageData >= 3X There is a 4.74% of reference with a coverageData >= 4X There is a 2.76% of reference with a coverageData >= 5X There is a 1.68% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% 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 0.01% 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 184262392 0.7392655282491754 7.409981917601539 chr2 243199373 168728100 0.6937850945857497 6.5088606473081425 chr3 198022430 161829378 0.8172275130650604 1.615254802504157 chr4 191154276 122747818 0.6421400586403833 3.49481443664985 chr5 180915260 96640241 0.5341740713304118 1.2746675564573615 chr6 171115067 189825521 1.1093442811789331 9.82942850696717 chr7 159138663 103708911 0.6516889676269305 7.982646080945196 chr8 146364022 160079355 1.0937069972018123 3.465101358303392 chr9 141213431 92321790 0.6537748523368149 8.040524429763598 chr10 135534747 123123332 0.908426324062862 15.939614804098111 chr11 135006516 110948078 0.8217979493671254 7.564478421518008 chr12 133851895 102732469 0.7675085137942949 1.5481659934630607 chr13 115169878 70145238 0.6090588895127595 1.3248591215647303 chr14 107349540 56358463 0.524999576150955 1.663581252178384 chr15 102531392 41096807 0.40082170151362034 1.1203849505096513 chr16 90354753 51425552 0.5691515973708655 6.648619593917024 chr17 81195210 50521659 0.6222246238417266 8.652402328806753 chr18 78077248 77321911 0.9903257732649593 9.592449209213042 chr19 59128983 35159221 0.5946190720039951 4.5546997069458826 chr20 63025520 58119814 0.9221631808829185 1.9247998993675843 chr21 48129895 28022632 0.5822292361119841 2.0964549747168717 chr22 51304566 18716248 0.36480667237298137 1.0835701712350065 chrMT 16571 355431 21.448977128718845 13.578472291140956 chrX 155270560 141217018 0.9094899767219233 4.138689135193892 chrY 59373566 4675926 0.07875433993639526 3.4549299514956684