BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819117.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,976,775 number of mapped reads = 1,801,111 (91.11%) number of supplementary alignments = 5,506 (0.28%) number of secondary alignments = 0 number of mapped bases = 104,381,844 bp number of sequenced bases = 104,349,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,838 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7926 >>>>>>> ACTG content number of A's = 27,134,472 bp (26%) number of C's = 19,457,487 bp (18.65%) number of T's = 31,918,081 bp (30.59%) number of G's = 25,837,495 bp (24.76%) number of N's = 1,489 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 538,583 number of insertions = 7,941 mapped reads with insertion percentage = 0.44% number of deletions = 19,661 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 0.3094X There is a 2.97% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10258244 0.04115634279603259 0.568338486080133 chr2 243199373 8263258 0.0339772997687786 0.3822544226482394 chr3 198022430 5736076 0.0289667993671222 0.19247112485061765 chr4 191154276 5760886 0.030137364021090483 0.21818902763206027 chr5 180915260 5666507 0.03132133242933736 0.19834151531779734 chr6 171115067 4519471 0.026411882245296378 0.23784536337620305 chr7 159138663 5186968 0.032594015195414834 0.40095440772652086 chr8 146364022 9557254 0.06529783665004778 0.3399944234719691 chr9 141213431 4457957 0.03156893057856515 0.25835502257644694 chr10 135534747 5419068 0.0399828687473036 0.30004938280745036 chr11 135006516 3611409 0.026749886649915476 0.287155241420393 chr12 133851895 4888147 0.036519072068423086 0.2143502159132802 chr13 115169878 2298130 0.01995426269358382 0.15668469815335456 chr14 107349540 2503663 0.02332253123767461 0.17465354236590896 chr15 102531392 2772820 0.027043619967629037 0.1972573555833393 chr16 90354753 3298065 0.03650128953371164 0.22793987597732832 chr17 81195210 3686107 0.045398084443651295 0.2536855478729487 chr18 78077248 2465793 0.03158145379304352 0.48769322338336657 chr19 59128983 2188646 0.03701477497084636 0.3805073562130928 chr20 63025520 2930835 0.04650235333242788 0.24241675539880314 chr21 48129895 1445800 0.030039541952044568 0.21441043167273074 chr22 51304566 877488 0.017103506927629016 0.14432487677962416 chrMT 16571 3782 0.22823004043208014 0.565798172041479 chrX 155270560 6247518 0.04023633327528412 0.25024095604895163 chrY 59373566 337952 0.005691960627731203 0.15597303758639702