BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971314.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 = 13,342,920 number of mapped reads = 12,371,101 (92.72%) number of supplementary alignments = 2,038 (0.02%) number of secondary alignments = 0 number of mapped bases = 592,767,426 bp number of sequenced bases = 592,639,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,393,225 duplication rate = 9.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.5237 >>>>>>> ACTG content number of A's = 166,454,273 bp (28.09%) number of C's = 126,222,346 bp (21.3%) number of T's = 169,789,815 bp (28.65%) number of G's = 130,140,183 bp (21.96%) number of N's = 33,363 bp (0.01%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 3,038,964 number of insertions = 39,721 mapped reads with insertion percentage = 0.32% number of deletions = 87,738 mapped reads with deletion percentage = 0.71% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.1915X std coverageData = 1.8178X There is a 12.36% of reference with a coverageData >= 1X There is a 3.98% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 47312366 0.18981844783447901 3.5271994622518426 chr2 243199373 50031422 0.20572183794240292 1.5950342142832978 chr3 198022430 40576952 0.20491088812514824 0.6636428603321052 chr4 191154276 40271168 0.2106736445696878 0.9871077383817459 chr5 180915260 36277107 0.200519884281735 0.6664475160519653 chr6 171115067 34422349 0.2011649213800676 0.7287211861319385 chr7 159138663 32627434 0.20502518611709086 2.8242274329463255 chr8 146364022 29834753 0.20383939025671213 3.431259256568644 chr9 141213431 24800480 0.175624087768252 1.6369310753026225 chr10 135534747 29284940 0.2160696105479136 1.9025167571437263 chr11 135006516 26447403 0.19589723358241465 1.3198238664559478 chr12 133851895 27378636 0.20454425393080913 0.715943231957799 chr13 115169878 19047393 0.16538519733432383 0.5712808940216159 chr14 107349540 18292878 0.17040481030472976 0.91884855595716 chr15 102531392 16890429 0.1647342211056688 0.5987687313848831 chr16 90354753 17291008 0.19136799588174405 0.8721219890967545 chr17 81195210 16329412 0.201112996690322 0.895754237564948 chr18 78077248 17963380 0.2300718898289038 3.2263500605058755 chr19 59128983 13140459 0.2222338070654792 2.988730727374711 chr20 63025520 12251334 0.19438687693493048 0.7082095875290435 chr21 48129895 7829214 0.1626684205315636 0.9781663099001661 chr22 51304566 6701303 0.1306180623377654 0.6633849190888313 chrMT 16571 65077 3.9271619093597248 3.64190557745104 chrX 155270560 22126556 0.14250322791390718 0.8068148604828116 chrY 59373566 5573973 0.09387970734316345 0.9708218437398871