BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081745.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 = 2,408,084 number of mapped reads = 2,203,819 (91.52%) number of supplementary alignments = 16,241 (0.67%) number of secondary alignments = 0 number of mapped bases = 148,414,843 bp number of sequenced bases = 148,355,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,769 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2478 >>>>>>> ACTG content number of A's = 40,704,271 bp (27.44%) number of C's = 28,606,772 bp (19.28%) number of T's = 45,250,510 bp (30.5%) number of G's = 33,791,761 bp (22.78%) number of N's = 1,697 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,215,381 number of insertions = 11,165 mapped reads with insertion percentage = 0.5% number of deletions = 33,556 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.4594X There is a 4.15% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11780433 0.047263404812138865 0.9146432466806237 chr2 243199373 12614454 0.051868776816295495 0.562101463845113 chr3 198022430 9942592 0.050209423245639394 0.25663887867207913 chr4 191154276 9735430 0.05092970036411846 0.2919455581274915 chr5 180915260 9060547 0.05008171781639647 0.2507536695335087 chr6 171115067 8438115 0.04931251904310682 0.2975468274332674 chr7 159138663 8302387 0.05217077260476921 0.6256142686853862 chr8 146364022 7506209 0.05128452264040681 0.5049362945270858 chr9 141213431 6271254 0.04440975589637788 0.4125040108331433 chr10 135534747 7106439 0.052432598704743955 0.525804899849012 chr11 135006516 6703592 0.049653840411673165 0.34734650911319015 chr12 133851895 6726990 0.05025696498357382 0.255345191462178 chr13 115169878 4653898 0.04040898610659291 0.22298495006590247 chr14 107349540 4554126 0.042423339680822104 0.25944899950990674 chr15 102531392 4209339 0.041054148567494335 0.2309720389317593 chr16 90354753 4295847 0.04754422824884486 0.3017813842030753 chr17 81195210 3999868 0.04926236412221854 0.2740116445398008 chr18 78077248 3900892 0.049961955626304864 0.7264255099479923 chr19 59128983 3131882 0.052966951926096885 0.6581743216441677 chr20 63025520 2919129 0.04631661904574528 0.25336984727869216 chr21 48129895 1903420 0.03954756186357772 0.25370513732960553 chr22 51304566 1647380 0.03210981260420369 0.19903856812986265 chrMT 16571 1126 0.06795003319051354 0.2870579817263733 chrX 155270560 8578770 0.05525046087294333 0.3076513415699772 chrY 59373566 430724 0.007254474154373682 0.20283723883085025