BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068108.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 = 3,483,157 number of mapped reads = 3,291,029 (94.48%) number of supplementary alignments = 18,608 (0.53%) number of secondary alignments = 0 number of mapped bases = 212,002,380 bp number of sequenced bases = 211,910,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 343,687 duplication rate = 9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8681 >>>>>>> ACTG content number of A's = 55,878,121 bp (26.37%) number of C's = 37,495,161 bp (17.69%) number of T's = 69,642,483 bp (32.86%) number of G's = 48,871,150 bp (23.06%) number of N's = 23,983 bp (0.01%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,138,953 number of insertions = 13,601 mapped reads with insertion percentage = 0.41% number of deletions = 51,508 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.0685X std coverageData = 0.663X There is a 5.31% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% 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 20131931 0.08076983286633416 1.5238875069695375 chr2 243199373 24201173 0.09951165869165296 0.995309103655296 chr3 198022430 12527215 0.06326159617372638 0.3112790329075848 chr4 191154276 15547634 0.08133552816783444 0.363498603352841 chr5 180915260 12590157 0.06959145955957502 0.33043384675138576 chr6 171115067 13628158 0.07964323796220703 0.4579242439120042 chr7 159138663 14275819 0.08970679237137992 0.4017667149340908 chr8 146364022 3565798 0.024362530841083335 0.7738889466204664 chr9 141213431 8348993 0.059123221784760684 0.5058589650907435 chr10 135534747 11620313 0.08573678157970811 0.5122975411561258 chr11 135006516 9453187 0.07002022776441398 0.35897988917716644 chr12 133851895 11236180 0.08394487056010676 0.38328658068285354 chr13 115169878 7036833 0.06109959585092206 0.3300424644595708 chr14 107349540 2678650 0.024952598772197812 0.28798385902580664 chr15 102531392 2796508 0.027274651650101463 0.2494706522642024 chr16 90354753 4722286 0.05226383608176097 0.33074766368159764 chr17 81195210 7793840 0.09598891363172778 0.38543302268112817 chr18 78077248 3166236 0.04055260759190693 0.9209555921717653 chr19 59128983 5259444 0.08894866329765895 0.9808758532927774 chr20 63025520 4665680 0.07402842531088993 0.3542451531465029 chr21 48129895 3661314 0.07607151438830274 0.3580301970963064 chr22 51304566 1955123 0.03810816760441946 0.23626926994836292 chrMT 16571 130627 7.882867660370527 5.276470550173364 chrX 155270560 10536527 0.06785914213228832 0.36062398288017944 chrY 59373566 472754 0.00796236493526429 0.3108440275379566