BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038454.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,421,516 number of mapped reads = 14,013,680 (97.17%) number of supplementary alignments = 371,073 (2.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,076,612 number of mapped paired reads (second in pair) = 6,937,068 number of mapped paired reads (both in pair) = 13,845,674 number of mapped paired reads (singletons) = 168,006 number of mapped bases = 1,977,778,249 bp number of sequenced bases = 1,976,115,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,614,097 duplication rate = 10.03% >>>>>>> Insert size mean insert size = 147,583.2399 std insert size = 3,565,081.3004 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.474 >>>>>>> ACTG content number of A's = 578,764,494 bp (29.29%) number of C's = 397,145,534 bp (20.1%) number of T's = 584,170,906 bp (29.56%) number of G's = 415,992,633 bp (21.05%) number of N's = 41,839 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 30,839,740 number of insertions = 445,206 mapped reads with insertion percentage = 2.93% number of deletions = 764,891 mapped reads with deletion percentage = 5.2% homopolymer indels = 45.12% >>>>>>> Coverage mean coverageData = 0.6389X std coverageData = 12.682X There is a 25.31% of reference with a coverageData >= 1X There is a 13.51% of reference with a coverageData >= 2X There is a 7.14% of reference with a coverageData >= 3X There is a 4.21% of reference with a coverageData >= 4X There is a 2.47% of reference with a coverageData >= 5X There is a 1.53% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 153813434 0.6171035136558396 15.556802668147482 chr2 243199373 196343206 0.8073343429220108 17.638190761942464 chr3 198022430 130684224 0.6599465727190602 1.5585170346288337 chr4 191154276 153266597 0.8017952839307659 13.5852818171899 chr5 180915260 109028153 0.602647631824977 1.7036867949064887 chr6 171115067 122562759 0.716259305207764 5.991190055499067 chr7 159138663 96030253 0.6034376008299127 8.951580551742671 chr8 146364022 80989739 0.5533445849144539 3.2454171908805707 chr9 141213431 83440354 0.5908811464257957 28.357035441630305 chr10 135534747 117753917 0.8688098041751611 22.931414330671767 chr11 135006516 86256836 0.6389086879332551 8.890111619227387 chr12 133851895 73747075 0.5509602609660476 1.4795991575890797 chr13 115169878 76555827 0.6647209177385774 1.525216973140374 chr14 107349540 61618723 0.5740008108092498 1.7592015511073478 chr15 102531392 47202713 0.4603732776787035 1.2335463917211311 chr16 90354753 59143263 0.6545672589022516 8.410471784605138 chr17 81195210 43625896 0.5372964242595099 9.901387274827794 chr18 78077248 62412611 0.7993700162177847 23.442269588175524 chr19 59128983 24913366 0.42133932863347234 8.189522330340862 chr20 63025520 44636069 0.7082221455689696 4.408293527356209 chr21 48129895 27143574 0.5639649535906945 6.337131084827573 chr22 51304566 14980857 0.2919985133486949 1.3424004019676041 chrMT 16571 6604323 398.5470400096554 224.3423549839858 chrX 155270560 53288254 0.34319612166015245 2.539006881849251 chrY 59373566 51736226 0.8713680091237909 25.844287762253668