BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237796.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,512,355 number of mapped reads = 2,211,093 (88.01%) number of supplementary alignments = 23,554 (0.94%) number of secondary alignments = 0 number of mapped bases = 149,697,271 bp number of sequenced bases = 149,634,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,593 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4009 >>>>>>> ACTG content number of A's = 41,648,672 bp (27.83%) number of C's = 28,291,858 bp (18.91%) number of T's = 46,548,272 bp (31.11%) number of G's = 32,888,295 bp (21.98%) number of N's = 257,504 bp (0.17%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,237,038 number of insertions = 10,807 mapped reads with insertion percentage = 0.48% number of deletions = 35,626 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.5414X There is a 2.37% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 12116697 0.048612504760820636 1.0411793236275109 chr2 243199373 11547839 0.047483013042143 0.5342627799345183 chr3 198022430 8840036 0.04464158933914709 0.3790699868265767 chr4 191154276 7945466 0.041565724640133084 0.37227449023855214 chr5 180915260 8363629 0.04622953862487885 0.38156076997288024 chr6 171115067 7216078 0.042170909473448065 0.40075476944109834 chr7 159138663 9046271 0.05684521177609743 0.650199438678041 chr8 146364022 8642842 0.05905031770717533 0.5733357467958864 chr9 141213431 8884164 0.06291302418677158 0.5333397894773456 chr10 135534747 5709969 0.04212918920341512 0.5192207409949238 chr11 135006516 5511695 0.04082539986440358 0.4124750405917534 chr12 133851895 5396725 0.04031862978107258 0.35995387229990067 chr13 115169878 6060529 0.05262251819004271 0.40940753986245565 chr14 107349540 6740721 0.06279226720487112 0.4699342857523824 chr15 102531392 4849126 0.04729406190057383 0.3910114181516441 chr16 90354753 5336291 0.05905932806877354 0.46576027400215514 chr17 81195210 3709630 0.045687793651866905 0.40230774101108374 chr18 78077248 3644662 0.04668020573675957 0.7966283884314753 chr19 59128983 6445917 0.10901450816429567 0.8229531444549808 chr20 63025520 2322929 0.03685695889538079 0.3465387310613447 chr21 48129895 1777431 0.03692987487298695 0.34694022394847424 chr22 51304566 1308149 0.025497711061428723 0.271913266105074 chrMT 16571 43557 2.628507633818116 3.154391141249532 chrX 155270560 7849584 0.05055423256024838 0.41080529618774403 chrY 59373566 387334 0.006523677557113547 0.16218613331395468