BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068166.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 = 1,678,054 number of mapped reads = 1,453,439 (86.61%) number of supplementary alignments = 11,653 (0.69%) number of secondary alignments = 0 number of mapped bases = 99,224,806 bp number of sequenced bases = 99,183,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,410 duplication rate = 7.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4484 >>>>>>> ACTG content number of A's = 28,590,851 bp (28.83%) number of C's = 18,962,217 bp (19.12%) number of T's = 30,839,709 bp (31.09%) number of G's = 20,686,729 bp (20.86%) number of N's = 103,505 bp (0.1%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 805,733 number of insertions = 6,830 mapped reads with insertion percentage = 0.47% number of deletions = 23,551 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.53% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.3725X There is a 1.53% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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 6884536 0.027620938204202108 0.4188298548827551 chr2 243199373 9460953 0.03890204519565106 0.4288538241037544 chr3 198022430 8188042 0.04134906333590594 0.39499202960649266 chr4 191154276 8621980 0.04510482412645585 0.408589292745872 chr5 180915260 3219316 0.017794607265302 0.23117315298048172 chr6 171115067 6663034 0.038938908868849056 0.4129128795787789 chr7 159138663 5383551 0.03382930897188699 0.3974793099145138 chr8 146364022 4608565 0.03148700710069309 0.45050162934237264 chr9 141213431 2464478 0.017452150142857163 0.27587775012294113 chr10 135534747 5251311 0.038745127107515834 0.4376743833053362 chr11 135006516 3477908 0.02576103808204339 0.33622549909084504 chr12 133851895 5021597 0.03751606953341975 0.3553059624205086 chr13 115169878 2286606 0.01985420180787202 0.26305776991728547 chr14 107349540 2799642 0.026079683247827612 0.29759032479084996 chr15 102531392 1991921 0.01942742570002366 0.25002435387766264 chr16 90354753 5117953 0.05664287522317725 0.4628902087955527 chr17 81195210 2177484 0.026817887409860755 0.3003890020506174 chr18 78077248 3973018 0.050885733062722704 0.5174703080578182 chr19 59128983 1889611 0.03195744124332394 0.3753563719532143 chr20 63025520 2087953 0.033128691361848345 0.3498777019436652 chr21 48129895 1175516 0.02442382224187275 0.28772136066705767 chr22 51304566 949084 0.01849901624740379 0.2535668029974565 chrMT 16571 16387 0.9888962645585662 1.5272500115532848 chrX 155270560 5359812 0.034519177363693414 0.3601276418826058 chrY 59373566 154548 0.002602976550204177 0.08222136177379408