BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080810.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 = 2,636,127 number of mapped reads = 2,400,403 (91.06%) number of supplementary alignments = 21,985 (0.83%) number of secondary alignments = 0 number of mapped bases = 163,324,139 bp number of sequenced bases = 163,260,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,014 duplication rate = 5.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.116 >>>>>>> ACTG content number of A's = 46,646,923 bp (28.57%) number of C's = 30,138,793 bp (18.46%) number of T's = 51,883,852 bp (31.78%) number of G's = 34,567,956 bp (21.17%) number of N's = 23,068 bp (0.01%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,324,059 number of insertions = 12,294 mapped reads with insertion percentage = 0.51% number of deletions = 35,743 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.3908X There is a 4.08% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 12722412 0.05104264915753209 0.5099000382436424 chr2 243199373 13984395 0.05750177242438861 0.4349139246725809 chr3 198022430 10902384 0.05505630852020148 0.28939423136980125 chr4 191154276 11065932 0.057890057348233215 0.3177995026719375 chr5 180915260 10151145 0.05610994340665348 0.2906233600745186 chr6 171115067 9847279 0.05754770268126067 0.3677984173362157 chr7 159138663 9404327 0.0590951741249705 0.5313236388152398 chr8 146364022 8794620 0.060087307521516455 0.6771554030171757 chr9 141213431 6481937 0.04590170321688452 0.3349772498548776 chr10 135534747 7649030 0.05643593373144379 0.43840879049090237 chr11 135006516 7234698 0.05358776905256928 0.31439444635258335 chr12 133851895 7379905 0.05513485632758505 0.29329627641991823 chr13 115169878 5473454 0.04752504817275226 0.2682553849660327 chr14 107349540 5130684 0.047794187101314084 0.2766105623304149 chr15 102531392 4445046 0.043353024993555145 0.2551052384807072 chr16 90354753 4392835 0.048617641619804995 0.3028535092446855 chr17 81195210 3867744 0.04763512527401555 0.28120161582169967 chr18 78077248 4640098 0.059429579280253324 0.6125753626949616 chr19 59128983 2671263 0.04517688051560095 0.4396304787552036 chr20 63025520 3288394 0.05217559490187467 0.28740669403903885 chr21 48129895 2197448 0.045656613213056044 0.28204784081539624 chr22 51304566 1532429 0.029869251793300425 0.21119466586664454 chrMT 16571 9622 0.5806529479210669 0.9765039216743483 chrX 155270560 9598358 0.061816985782752375 0.32328659667732845 chrY 59373566 458700 0.007725660271104485 0.20762367929608674