BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548947.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,455,876 number of mapped reads = 4,764,872 (87.33%) number of secondary alignments = 0 number of mapped bases = 188,362,415 bp number of sequenced bases = 188,343,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 192,150 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.4842 >>>>>>> ACTG content number of A's = 53,002,344 bp (28.14%) number of C's = 40,599,053 bp (21.56%) number of T's = 54,172,146 bp (28.76%) number of G's = 40,568,109 bp (21.54%) number of N's = 1,549 bp (0%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 574,480 number of insertions = 6,424 mapped reads with insertion percentage = 0.13% number of deletions = 14,670 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.32% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.6489X There is a 5.26% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15238151 0.061135859717677495 1.0964097859930348 chr2 243199373 16041405 0.0659598945594321 0.5305186797238266 chr3 198022430 12707642 0.06417274043147536 0.28580381890860707 chr4 191154276 12464566 0.06520683848055797 0.312168707597169 chr5 180915260 11627603 0.06427099073897913 0.2902581064176552 chr6 171115067 11067185 0.0646768586427284 0.30950509076043586 chr7 159138663 11008461 0.06917527640658888 0.9144931372598535 chr8 146364022 9852445 0.06731466425540014 1.653944161533711 chr9 141213431 8025183 0.05683016794627701 0.5545696701504302 chr10 135534747 8965317 0.06614773848362294 0.4699109498284571 chr11 135006516 8658119 0.06413111941945084 0.40524778757295465 chr12 133851895 8688097 0.0649082853851266 0.3076324995018985 chr13 115169878 6050848 0.05253845975247104 0.2510389406350564 chr14 107349540 5838517 0.0543879088815844 0.3350250078247395 chr15 102531392 5332827 0.0520116512219009 0.2577385953823797 chr16 90354753 5305702 0.058720784727284904 0.32637809024128855 chr17 81195210 5150279 0.06343082307441535 0.29679695072171364 chr18 78077248 5039502 0.06454507720354077 1.0154475832859455 chr19 59128983 4215850 0.0712992137882703 1.0436050567135224 chr20 63025520 3846512 0.0610310236234465 0.29636168811751734 chr21 48129895 2379923 0.04944791589510012 0.3322800114801772 chr22 51304566 2183262 0.04255492581303582 0.31841252511787216 chrMT 16571 8597 0.5187978999456883 0.9916340189445025 chrX 155270560 6904817 0.044469582643354925 0.33864697390179416 chrY 59373566 1761605 0.029669853415912394 0.30248017545488204