BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548939.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 = 3,371,643 number of mapped reads = 2,947,682 (87.43%) number of secondary alignments = 0 number of mapped bases = 116,435,796 bp number of sequenced bases = 116,423,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,238 duplication rate = 1.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.5103 >>>>>>> ACTG content number of A's = 33,895,153 bp (29.11%) number of C's = 24,269,464 bp (20.85%) number of T's = 34,053,925 bp (29.25%) number of G's = 24,203,617 bp (20.79%) number of N's = 939 bp (0%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 386,805 number of insertions = 4,344 mapped reads with insertion percentage = 0.15% number of deletions = 9,794 mapped reads with deletion percentage = 0.33% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.4829X There is a 3.39% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% 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 8977198 0.03601675279276435 0.5164520253868863 chr2 243199373 9606771 0.03950162733355402 0.33206822083331344 chr3 198022430 7741220 0.03909264218199928 0.2137568352018314 chr4 191154276 7662285 0.04008429819273308 0.224198403946896 chr5 180915260 9058404 0.05006987249168478 0.2452392039679921 chr6 171115067 6706572 0.03919334584370644 0.22886657241571057 chr7 159138663 6451362 0.04053924972336861 0.4665197702393734 chr8 146364022 5969273 0.04078374533872812 1.6978752437198021 chr9 141213431 4792152 0.03393552558042443 0.3358911776528856 chr10 135534747 5265984 0.03885338716867934 0.28877057078961454 chr11 135006516 5196493 0.03849068292377829 0.32049792364533863 chr12 133851895 5227775 0.039056413807215806 0.22319346509763044 chr13 115169878 3687799 0.032020516684058656 0.19081627621119407 chr14 107349540 3490233 0.03251278952848797 0.23001027225440082 chr15 102531392 3199623 0.031206276805449008 0.19080971794377816 chr16 90354753 3088389 0.03418070325531187 0.22277803320820821 chr17 81195210 2909570 0.035834256725242784 0.21471959536098245 chr18 78077248 3026925 0.038768336199554575 0.6016667256435198 chr19 59128983 2341501 0.039599886235148 0.5334374918667758 chr20 63025520 2207913 0.0350320473357459 0.20874910360023236 chr21 48129895 1422568 0.029556848191752756 0.21198164390641808 chr22 51304566 1211003 0.023604195384870814 0.18393591258689643 chrMT 16571 3997 0.2412045139098425 0.5345413447177141 chrX 155270560 6761895 0.043549111950134015 0.2687840210336128 chrY 59373566 428891 0.00722360182981093 0.1147084811428886