BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085089.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 = 2,666,392 number of mapped reads = 2,200,413 (82.52%) number of supplementary alignments = 14,060 (0.53%) number of secondary alignments = 0 number of mapped bases = 132,159,802 bp number of sequenced bases = 132,115,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,713 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.585 >>>>>>> ACTG content number of A's = 38,302,115 bp (28.99%) number of C's = 25,790,024 bp (19.52%) number of T's = 39,163,628 bp (29.64%) number of G's = 28,856,260 bp (21.84%) number of N's = 3,053 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,114,556 number of insertions = 9,920 mapped reads with insertion percentage = 0.45% number of deletions = 27,889 mapped reads with deletion percentage = 1.26% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0427X std coverageData = 0.3382X There is a 3.76% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10748362 0.043122709010221486 0.606515671179421 chr2 243199373 11423028 0.04696980859403778 0.3698124437540935 chr3 198022430 9140576 0.046159296196900526 0.23858314043682535 chr4 191154276 8960792 0.04687727728361148 0.24868409573124817 chr5 180915260 8350086 0.04615468037356274 0.23753411243683026 chr6 171115067 7513058 0.04390646675198976 0.2891844984212939 chr7 159138663 7127014 0.0447849307367877 0.3280134559183001 chr8 146364022 6509643 0.04447570455531756 0.4707400418907443 chr9 141213431 5695367 0.04033162397987483 0.3042028099206689 chr10 135534747 6184877 0.045633146753134825 0.35735372077785454 chr11 135006516 5883178 0.04357699298010179 0.2926736351580467 chr12 133851895 5944335 0.04440979337647778 0.23579356445700664 chr13 115169878 4224454 0.03668019861929523 0.2100488045881251 chr14 107349540 3713499 0.034592593503428144 0.22122860892701537 chr15 102531392 3771185 0.03678078417193439 0.21199064861138156 chr16 90354753 3565964 0.03946625807277676 0.23832718967328867 chr17 81195210 3429754 0.04224084154717994 0.253088280361579 chr18 78077248 3628923 0.04647862332442865 0.5626835960710583 chr19 59128983 2484067 0.04201098808007572 0.4582374265201568 chr20 63025520 2524362 0.04005301344598188 0.23022466922828286 chr21 48129895 1771044 0.036797171487700106 0.21947438843917932 chr22 51304566 1422789 0.027732210033703433 0.18192247802716094 chrMT 16571 9002 0.5432381871944965 0.8354386008915353 chrX 155270560 7818210 0.0503521723628742 0.2767534426030549 chrY 59373566 316233 0.005326158108812261 0.11431043471032527