BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081919.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 = 2,894,457 number of mapped reads = 2,678,788 (92.55%) number of supplementary alignments = 18,697 (0.65%) number of secondary alignments = 0 number of mapped bases = 183,277,000 bp number of sequenced bases = 183,208,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,997 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2182 >>>>>>> ACTG content number of A's = 52,201,215 bp (28.49%) number of C's = 33,558,363 bp (18.32%) number of T's = 58,506,024 bp (31.93%) number of G's = 38,918,646 bp (21.24%) number of N's = 23,978 bp (0.01%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,374,399 number of insertions = 13,048 mapped reads with insertion percentage = 0.48% number of deletions = 38,588 mapped reads with deletion percentage = 1.43% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.5041X There is a 4.88% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 14483412 0.05810782714158213 0.8155625330385478 chr2 243199373 14927094 0.061378011858607875 0.5000351420042715 chr3 198022430 12931718 0.06530430921386027 0.3039284922631258 chr4 191154276 12298699 0.06433912574364803 0.30763013977291664 chr5 180915260 11208607 0.0619550114235803 0.2900124952901991 chr6 171115067 11423368 0.06675839948097616 0.3634270057090471 chr7 159138663 10787129 0.06778446416883621 0.6049025603554086 chr8 146364022 9238430 0.06311954176826325 1.1294001420210358 chr9 141213431 7899051 0.05593696678894517 0.43504529712649387 chr10 135534747 8486829 0.06261736704315389 0.5587550050794665 chr11 135006516 7972237 0.059050757224192056 0.35859510819096463 chr12 133851895 8615653 0.0643670603243981 0.29835340472428556 chr13 115169878 6246857 0.0542403717749879 0.27186669995160073 chr14 107349540 5774487 0.05379144614872127 0.28826426765809526 chr15 102531392 4967580 0.04844935685648352 0.25668839468628346 chr16 90354753 4640008 0.051353225435744373 0.3106645752475154 chr17 81195210 4310071 0.053082823481828544 0.28911249248829846 chr18 78077248 5168158 0.06619288118351713 0.7761429312247613 chr19 59128983 2762890 0.046726492826707336 0.6341990706176784 chr20 63025520 3483534 0.0552718010101305 0.2807624519779348 chr21 48129895 2356222 0.04895547767141399 0.27506153877712114 chr22 51304566 1594759 0.031084153406540853 0.20168536825677258 chrMT 16571 116478 7.029026612757226 4.402799380753238 chrX 155270560 11148271 0.07179900040290961 0.3471275592362256 chrY 59373566 435458 0.00733420660635408 0.15402627265104163