BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084337.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 = 2,443,714 number of mapped reads = 2,184,837 (89.41%) number of supplementary alignments = 14,390 (0.59%) number of secondary alignments = 0 number of mapped bases = 143,378,991 bp number of sequenced bases = 143,328,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,236 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4429 >>>>>>> ACTG content number of A's = 39,412,890 bp (27.5%) number of C's = 27,856,254 bp (19.44%) number of T's = 43,299,936 bp (30.21%) number of G's = 32,593,109 bp (22.74%) number of N's = 166,616 bp (0.12%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,456,333 number of insertions = 11,304 mapped reads with insertion percentage = 0.51% number of deletions = 31,111 mapped reads with deletion percentage = 1.41% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.3148X There is a 3.98% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14249702 0.05717017651883804 0.4613942084016518 chr2 243199373 12539731 0.05156152684653509 0.39451272369184864 chr3 198022430 9072895 0.0458175116828937 0.2431594463031084 chr4 191154276 6931494 0.03626125528052535 0.22122144128940335 chr5 180915260 7393767 0.0408686752018597 0.2272542673359342 chr6 171115067 6775262 0.03959477162814657 0.2551605793822538 chr7 159138663 8078427 0.05076344646680864 0.47037762998063165 chr8 146364022 7146591 0.048827511722792094 0.29444169232358425 chr9 141213431 5446740 0.03857097700572122 0.2652688064974994 chr10 135534747 10049119 0.0741442266461751 0.41582965440124875 chr11 135006516 8082161 0.059864969776718034 0.3281912178742392 chr12 133851895 7221517 0.05395154846332209 0.26354844496946667 chr13 115169878 3633675 0.03155056741485825 0.20026093828463257 chr14 107349540 3742806 0.03486559886516514 0.2161999058257169 chr15 102531392 3423934 0.03339400678379554 0.21523297307703584 chr16 90354753 3116789 0.03449501986907097 0.2296538258648156 chr17 81195210 4402794 0.05422479971417033 0.2781270700983092 chr18 78077248 3972019 0.050872938042078535 0.4180228510983802 chr19 59128983 3268098 0.05527066142842335 0.3789411854731769 chr20 63025520 2954990 0.046885610781156585 0.2468170418209346 chr21 48129895 1431867 0.029750054513935673 0.20198461793531922 chr22 51304566 1322897 0.02578517085594292 0.1785072680242361 chrMT 16571 6533 0.39424295455916963 0.7093094274327063 chrX 155270560 8803348 0.05669682649434638 0.2895285124883098 chrY 59373566 311835 0.0052520847408761 0.10489301473141407