BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818762.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 = 812,319 number of mapped reads = 778,829 (95.88%) number of supplementary alignments = 6,269 (0.77%) number of secondary alignments = 0 number of mapped bases = 52,819,910 bp number of sequenced bases = 52,799,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 279,087 duplication rate = 31.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7643 >>>>>>> ACTG content number of A's = 14,936,574 bp (28.29%) number of C's = 11,661,464 bp (22.09%) number of T's = 14,976,310 bp (28.36%) number of G's = 11,221,689 bp (21.25%) number of N's = 3,203 bp (0.01%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 261,462 number of insertions = 4,937 mapped reads with insertion percentage = 0.63% number of deletions = 13,117 mapped reads with deletion percentage = 1.67% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.2526X There is a 0.97% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 4386993 0.017600730471199106 0.3344308485537311 chr2 243199373 4731667 0.01945591775847218 0.3739726009748733 chr3 198022430 3556118 0.01795815756831183 0.21359493830670878 chr4 191154276 3478389 0.018196762702812883 0.22932542223964206 chr5 180915260 3314751 0.01832211942762595 0.2168471664813876 chr6 171115067 3150750 0.018413048337818202 0.22902425020456657 chr7 159138663 2882793 0.018114975617207492 0.24083920559847485 chr8 146364022 2741120 0.018728099723851536 0.23462334804871748 chr9 141213431 2262749 0.016023610388731367 0.2186147490268314 chr10 135534747 2544110 0.01877090603194176 0.25242454752237503 chr11 135006516 2517517 0.01864737402748768 0.23190157393123995 chr12 133851895 2418745 0.01807030823134779 0.22113097607379525 chr13 115169878 1710596 0.014852807259203661 0.19275733330455339 chr14 107349540 1647128 0.015343596255745483 0.21019517780578867 chr15 102531392 1519130 0.014816242814688402 0.1942301993839267 chr16 90354753 1598270 0.017688831488477424 0.2781092383258772 chr17 81195210 1323395 0.016298929456552917 0.21030000114574415 chr18 78077248 1403119 0.01797090747870622 0.2663334309859976 chr19 59128983 1021112 0.017269229880040385 0.288759569862738 chr20 63025520 1131687 0.017956012104303146 0.22414458413693303 chr21 48129895 706980 0.014688999425409093 0.19925131074826535 chr22 51304566 672018 0.013098600229850887 0.19740193831504665 chrMT 16571 23935 1.4443908032104278 2.171470175902024 chrX 155270560 1574849 0.010142611709521753 0.16380167067385246 chrY 59373566 501989 0.00845475577464894 0.3496014433093704