BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975302.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,449,046 number of mapped reads = 2,423,456 (98.96%) number of supplementary alignments = 25,058 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,213,139 number of mapped paired reads (second in pair) = 1,210,317 number of mapped paired reads (both in pair) = 2,416,690 number of mapped paired reads (singletons) = 6,766 number of mapped bases = 327,508,184 bp number of sequenced bases = 327,298,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,606 duplication rate = 15.25% >>>>>>> Insert size mean insert size = 68,882.9802 std insert size = 2,557,841.7644 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.6718 >>>>>>> ACTG content number of A's = 95,675,894 bp (29.23%) number of C's = 66,353,166 bp (20.27%) number of T's = 95,676,408 bp (29.23%) number of G's = 69,572,496 bp (21.26%) number of N's = 20,785 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,188,773 number of insertions = 55,824 mapped reads with insertion percentage = 2.2% number of deletions = 112,737 mapped reads with deletion percentage = 4.5% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.1058X std coverageData = 1.1589X There is a 5.97% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.22% 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 0.01% 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 0.01% 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% 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 30760969 0.12341381087271193 1.2312601486023567 chr2 243199373 28116107 0.11560929065388668 1.31711831742794 chr3 198022430 17764421 0.08970913547520853 0.4313725298914083 chr4 191154276 21384812 0.11187200436991532 0.801522226476892 chr5 180915260 20333360 0.11239162467555253 0.46724095006960353 chr6 171115067 26800292 0.15662146221174084 1.0303661968546634 chr7 159138663 18931246 0.11896069530256138 1.2342780116112575 chr8 146364022 17108791 0.11689205288441719 0.598161770849926 chr9 141213431 14526038 0.10286583859009842 2.0186136221443793 chr10 135534747 18064100 0.13328021337583637 2.8411925433674243 chr11 135006516 12123152 0.08979679173411156 1.1643132473699855 chr12 133851895 14614406 0.10918340752665474 0.4594838972716711 chr13 115169878 11242687 0.09761829390841241 0.4374867982754923 chr14 107349540 9805160 0.0913386307943192 0.4268200639271439 chr15 102531392 9616163 0.09378750071002645 0.4272680966048991 chr16 90354753 10859596 0.12018843103915075 1.589583668543186 chr17 81195210 7006038 0.0862863462019496 0.9622258707422948 chr18 78077248 9385084 0.12020254607334521 1.8566044261877046 chr19 59128983 4394964 0.07432842198554303 0.8037106844955528 chr20 63025520 7098861 0.11263470733759912 0.5182380332356036 chr21 48129895 2919845 0.06066593330403069 0.5351161930236177 chr22 51304566 3386971 0.06601695061605238 0.3596351840380575 chrMT 16571 35359 2.1337879427916238 2.399512588781107 chrX 155270560 10457855 0.06735246527094382 0.5016176675877347 chrY 59373566 771907 0.013000852938494548 0.9342059824964556