BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083659.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,051,801 number of mapped reads = 1,671,095 (81.45%) number of supplementary alignments = 11,094 (0.54%) number of secondary alignments = 0 number of mapped bases = 101,838,966 bp number of sequenced bases = 101,806,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,680 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5681 >>>>>>> ACTG content number of A's = 30,542,044 bp (30%) number of C's = 19,587,202 bp (19.24%) number of T's = 29,844,928 bp (29.32%) number of G's = 21,818,647 bp (21.43%) number of N's = 13,956 bp (0.01%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 837,024 number of insertions = 7,052 mapped reads with insertion percentage = 0.42% number of deletions = 20,011 mapped reads with deletion percentage = 1.19% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2846X There is a 2.96% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10862107 0.04357905692038376 0.6440044115326041 chr2 243199373 8393279 0.03451192696948277 0.23184382447584698 chr3 198022430 9379178 0.047364220305750215 0.23813149821126114 chr4 191154276 5421813 0.028363545474651062 0.1827254820030787 chr5 180915260 5232320 0.02892138562551329 0.1838822707850803 chr6 171115067 6431023 0.03758303177358426 0.23802259433101594 chr7 159138663 7692003 0.048335224482814715 0.34743298695663344 chr8 146364022 7367322 0.050335607749286915 0.35051341944701975 chr9 141213431 3591140 0.025430583865638106 0.19091426497951516 chr10 135534747 4631480 0.03417190132062592 0.25702633265859665 chr11 135006516 3830223 0.028370652865377252 0.19673747531459382 chr12 133851895 3638532 0.027183268492388547 0.1791006538738161 chr13 115169878 3240037 0.02813267719186088 0.18029205042990315 chr14 107349540 2026561 0.018878152621799777 0.1493509234136849 chr15 102531392 2294347 0.022377019908205283 0.16143102290300662 chr16 90354753 2256814 0.024977258252258185 0.1752480876210392 chr17 81195210 1788834 0.022031274997626093 0.16537233985356162 chr18 78077248 2767016 0.035439466309058434 0.2771926006620917 chr19 59128983 2697616 0.04562256719348615 0.408326406125234 chr20 63025520 1817968 0.028844950426430437 0.18600864704383036 chr21 48129895 1595370 0.033147173913427405 0.1984089449979703 chr22 51304566 553478 0.010788084631687558 0.11038665441214633 chrMT 16571 5134 0.3098183573713113 0.6062759986714875 chrX 155270560 4143560 0.026686063346457952 0.18008988670323978 chrY 59373566 181811 0.0030621539558530137 0.06682985627706524