BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080797.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,186,155 number of mapped reads = 1,978,947 (90.52%) number of supplementary alignments = 16,551 (0.76%) number of secondary alignments = 0 number of mapped bases = 133,856,009 bp number of sequenced bases = 133,807,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,377 duplication rate = 5.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8056 >>>>>>> ACTG content number of A's = 37,761,285 bp (28.22%) number of C's = 24,579,848 bp (18.37%) number of T's = 42,740,071 bp (31.94%) number of G's = 28,708,197 bp (21.45%) number of N's = 17,964 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,076,666 number of insertions = 9,690 mapped reads with insertion percentage = 0.49% number of deletions = 27,669 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.3232X There is a 3.41% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 10444509 0.041903642839870796 0.3902740387706229 chr2 243199373 11356102 0.046694618739827096 0.3656326010437749 chr3 198022430 9314544 0.047037822937532885 0.2641708573698511 chr4 191154276 9147315 0.04785304933487337 0.27338638492237505 chr5 180915260 8154204 0.0450719524710077 0.2590726074713951 chr6 171115067 9039969 0.052829766299889884 0.35468695943364287 chr7 159138663 6861336 0.0431154558587689 0.3088545091498382 chr8 146364022 6926706 0.04732519580529155 0.5689863275643424 chr9 141213431 5508503 0.039008350416753206 0.2949554311155334 chr10 135534747 6055666 0.044679804507990854 0.335749091016511 chr11 135006516 6768284 0.050133017283402824 0.3072693796013585 chr12 133851895 5668788 0.04235119719448126 0.2532186445510589 chr13 115169878 4249832 0.036900551375073955 0.23369004108841043 chr14 107349540 3763807 0.035061230816638804 0.23793087161270982 chr15 102531392 3571055 0.03482889415955652 0.22770705174398023 chr16 90354753 3225031 0.035692986731976344 0.2481842745791886 chr17 81195210 2970905 0.03658965842935809 0.23958114411398293 chr18 78077248 3664137 0.04692963819626429 0.48387958663849157 chr19 59128983 2240428 0.03789052147235477 0.32296443248403156 chr20 63025520 2781870 0.04413878695487161 0.259921354346123 chr21 48129895 1700474 0.03533093101491287 0.24076979788688382 chr22 51304566 1258937 0.024538498191369554 0.1887522488518341 chrMT 16571 197555 11.921730734415545 6.604232164441368 chrX 155270560 8668035 0.055825360583487305 0.3043704245934027 chrY 59373566 318017 0.00535620515028523 0.11585657489751637