BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083652.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 = 2,250,211 number of mapped reads = 1,886,071 (83.82%) number of supplementary alignments = 12,963 (0.58%) number of secondary alignments = 0 number of mapped bases = 115,640,576 bp number of sequenced bases = 115,604,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,291 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2127 >>>>>>> ACTG content number of A's = 34,188,498 bp (29.57%) number of C's = 22,515,861 bp (19.48%) number of T's = 33,918,825 bp (29.34%) number of G's = 24,965,991 bp (21.6%) number of N's = 15,438 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 919,529 number of insertions = 7,906 mapped reads with insertion percentage = 0.42% number of deletions = 22,892 mapped reads with deletion percentage = 1.2% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.3077X There is a 3.34% of reference with a coverageData >= 1X There is a 0.31% 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% 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 10808286 0.04336312566298481 0.63935588166948 chr2 243199373 13452803 0.05531594442062974 0.3009220675328516 chr3 198022430 10395637 0.052497270132479436 0.2535917085410367 chr4 191154276 4664490 0.024401703679388265 0.1716924753883778 chr5 180915260 5435426 0.03004404382471661 0.18865506090906425 chr6 171115067 8700730 0.05084724654901371 0.28778452178922476 chr7 159138663 6526468 0.041011202915535366 0.3604987493304518 chr8 146364022 7549038 0.051577142366311855 0.4143805469598252 chr9 141213431 5240537 0.03711075471284314 0.23759306182105158 chr10 135534747 6026576 0.04446517320019788 0.34776497506209036 chr11 135006516 3789533 0.028069260005198562 0.20169557067855315 chr12 133851895 4089240 0.0305504826808765 0.19149379040906372 chr13 115169878 3576520 0.03105430050034437 0.19034746308772846 chr14 107349540 2324988 0.021658108642105035 0.16195814206395237 chr15 102531392 3010548 0.029362207430091262 0.18704315292243406 chr16 90354753 3493015 0.038658896007385465 0.2247518789292534 chr17 81195210 2320818 0.0285831885895732 0.18877788271601337 chr18 78077248 3100874 0.03971546230727804 0.3293072922772221 chr19 59128983 2495622 0.04220640831925014 0.44932236021936056 chr20 63025520 1837859 0.029160552741175322 0.18933063444901543 chr21 48129895 1741082 0.036174647794265914 0.21062990275660792 chr22 51304566 981513 0.01913110423738893 0.14928849667137892 chrMT 16571 13720 0.8279524470460443 1.0334794033906325 chrX 155270560 3862010 0.0248727769127644 0.1780032090107927 chrY 59373566 203243 0.0034231226738175033 0.07149088207107646