BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212678.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 = 1,477,658 number of mapped reads = 684,589 (46.33%) number of supplementary alignments = 6,310 (0.43%) number of secondary alignments = 0 number of mapped bases = 44,355,508 bp number of sequenced bases = 44,339,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 177,902 duplication rate = 13.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5909 >>>>>>> ACTG content number of A's = 12,322,883 bp (27.79%) number of C's = 8,371,059 bp (18.88%) number of T's = 13,941,115 bp (31.44%) number of G's = 9,703,625 bp (21.89%) number of N's = 428 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 415,241 number of insertions = 3,912 mapped reads with insertion percentage = 0.56% number of deletions = 9,584 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.4467X There is a 0.43% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 3451731 0.013848434905203306 0.47176908775897625 chr2 243199373 3776606 0.015528847601099694 0.49274903949966864 chr3 198022430 3283779 0.016582863870522144 0.44703075647437 chr4 191154276 2792123 0.014606646832216299 0.4659871277821096 chr5 180915260 2601661 0.014380550319525285 0.45631352681183573 chr6 171115067 2865363 0.01674524079168318 0.4551994059288174 chr7 159138663 2407229 0.015126613197699167 0.4491852476482474 chr8 146364022 2348782 0.01604753660021723 0.43720989587648285 chr9 141213431 1945125 0.013774362581700887 0.4123174871730725 chr10 135534747 2143595 0.015815833558902797 0.43720982858650426 chr11 135006516 1961271 0.014527232152261451 0.44326230365926717 chr12 133851895 1904818 0.014230788439715404 0.41205531231580517 chr13 115169878 1208655 0.010494540942380785 0.35244631050340797 chr14 107349540 1333087 0.012418190147810601 0.4988228187717844 chr15 102531392 1318277 0.012857301303390087 0.5219532961054083 chr16 90354753 1099134 0.01216465059674282 0.35710405466477846 chr17 81195210 1174869 0.014469683618036088 0.4299794058345221 chr18 78077248 1263691 0.016185137570422566 0.5471912330500768 chr19 59128983 770371 0.013028652970405393 0.37375264923100704 chr20 63025520 909867 0.014436485410989072 0.43812561205183037 chr21 48129895 738241 0.015338512581421588 0.40334024624682274 chr22 51304566 373694 0.007283835126877401 0.2488241772844402 chrMT 16571 10864 0.6556031621507453 3.103179594056103 chrX 155270560 2527513 0.016278121235603196 0.48528875818310774 chrY 59373566 145162 0.0024448927322303668 0.2111926816954385