BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 346,704 number of mapped reads = 329,342 (94.99%) number of supplementary alignments = 2,882 (0.83%) number of secondary alignments = 0 number of mapped bases = 22,295,856 bp number of sequenced bases = 22,286,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,976 duplication rate = 13.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.612 >>>>>>> ACTG content number of A's = 6,482,611 bp (29.09%) number of C's = 4,896,656 bp (21.97%) number of T's = 6,282,755 bp (28.19%) number of G's = 4,622,823 bp (20.74%) number of N's = 1,346 bp (0.01%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 116,483 number of insertions = 2,259 mapped reads with insertion percentage = 0.68% number of deletions = 5,737 mapped reads with deletion percentage = 1.72% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0072X std coverageData = 0.1244X There is a 0.58% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% 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 1864651 0.007481028502633099 0.1615115427415299 chr2 243199373 2010023 0.008264918511940406 0.19192760886827964 chr3 198022430 1502369 0.007586862760950868 0.1045177904406264 chr4 191154276 1407577 0.007363565332956507 0.11323010485721498 chr5 180915260 1379223 0.0076235857605378345 0.10604386680754271 chr6 171115067 1355571 0.00792198503478364 0.11286611997472507 chr7 159138663 1215160 0.007635856536007218 0.11273444788903932 chr8 146364022 1134067 0.007748263435941928 0.110907497447896 chr9 141213431 908536 0.0064337789512387104 0.10473010621623656 chr10 135534747 1095346 0.008081661892946169 0.12898210305727076 chr11 135006516 1019192 0.007549205995360994 0.11009734996085468 chr12 133851895 1020174 0.007621662734024049 0.107466764741007 chr13 115169878 707310 0.006141449589796387 0.09384597877952867 chr14 107349540 676733 0.006304013971554979 0.10039452858383 chr15 102531392 657892 0.006416493399406886 0.09708992676771395 chr16 90354753 686393 0.00759664519253348 0.13339316333112664 chr17 81195210 623963 0.007684726722179794 0.10775254241706571 chr18 78077248 589554 0.007550906507360506 0.12145164826236199 chr19 59128983 437758 0.007403442064951464 0.13157750551070957 chr20 63025520 500415 0.007939878956968542 0.11042541326194766 chr21 48129895 291001 0.006046159045225426 0.0950035059138554 chr22 51304566 283208 0.0055201324576062095 0.09277009509634039 chrMT 16571 18902 1.1406674310542515 1.4799557552994647 chrX 155270560 701317 0.004516741615409901 0.08523477940190353 chrY 59373566 209521 0.0035288599643821294 0.1914820299282753