BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083664.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 = 2,347,441 number of mapped reads = 1,926,007 (82.05%) number of supplementary alignments = 13,110 (0.56%) number of secondary alignments = 0 number of mapped bases = 116,884,000 bp number of sequenced bases = 116,847,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,849 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0364 >>>>>>> ACTG content number of A's = 35,053,862 bp (30%) number of C's = 22,660,630 bp (19.39%) number of T's = 34,320,936 bp (29.37%) number of G's = 24,796,706 bp (21.22%) number of N's = 14,920 bp (0.01%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 991,489 number of insertions = 7,834 mapped reads with insertion percentage = 0.4% number of deletions = 23,395 mapped reads with deletion percentage = 1.2% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3679X There is a 3.34% of reference with a coverageData >= 1X There is a 0.33% 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 10003477 0.04013421093943834 0.9226994614303271 chr2 243199373 14253016 0.058606302410162875 0.3164858119400061 chr3 198022430 9726293 0.04911712779203851 0.24544026212955125 chr4 191154276 5496684 0.028755223869540852 0.1884601995918247 chr5 180915260 7750249 0.0428391115265788 0.22742555789751853 chr6 171115067 9732139 0.05687482213357635 0.30631031725508595 chr7 159138663 7579215 0.047626484080741584 0.39036171655137825 chr8 146364022 8346096 0.05702286590621294 0.4044568264681758 chr9 141213431 4543659 0.03217582752450792 0.23009322936999338 chr10 135534747 4506934 0.03325297829345562 0.31065438538074813 chr11 135006516 2388207 0.017689568405720505 0.17127369088243494 chr12 133851895 4328502 0.03233799566304235 0.19832398408989985 chr13 115169878 3402565 0.029543879520303042 0.1868423843656117 chr14 107349540 2778258 0.025880483512085845 0.17706218432181586 chr15 102531392 2125445 0.02072970003177173 0.1580748507162354 chr16 90354753 3108142 0.034399319314170444 0.21701471768045222 chr17 81195210 2034657 0.02505883044085975 0.18024641854010243 chr18 78077248 3440058 0.044059672799942946 0.4073416546270374 chr19 59128983 2836886 0.04797792649334084 0.5640489007374498 chr20 63025520 1616070 0.025641517912109252 0.1803876753502044 chr21 48129895 1638059 0.034034127853385096 0.20428245242968726 chr22 51304566 607490 0.011840856425917335 0.11766840339187237 chrMT 16571 34749 2.09697664594774 1.7276502016136448 chrX 155270560 4374797 0.0281753153978449 0.1930632687360735 chrY 59373566 232353 0.003913408199197602 0.08686306664628067