BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124902.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,314,148 number of mapped reads = 5,191,544 (97.69%) number of supplementary alignments = 18,066 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,597,461 number of mapped paired reads (second in pair) = 2,594,083 number of mapped paired reads (both in pair) = 5,172,680 number of mapped paired reads (singletons) = 18,864 number of mapped bases = 471,266,364 bp number of sequenced bases = 470,990,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,582 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 40,794.904 std insert size = 1,924,631.5733 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.4127 >>>>>>> ACTG content number of A's = 134,337,725 bp (28.52%) number of C's = 91,219,138 bp (19.37%) number of T's = 139,157,909 bp (29.55%) number of G's = 106,269,088 bp (22.56%) number of N's = 6,692 bp (0%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 3,382,897 number of insertions = 53,725 mapped reads with insertion percentage = 1.01% number of deletions = 162,886 mapped reads with deletion percentage = 3.08% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.1522X std coverageData = 1.3483X There is a 9.79% of reference with a coverageData >= 1X There is a 2.94% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% 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 36723692 0.14733641125010477 1.6237971667199698 chr2 243199373 37589877 0.15456403746567224 1.6017019430662165 chr3 198022430 34412572 0.1737811822630396 0.597351748869424 chr4 191154276 26340141 0.13779519637844775 0.8049212786980005 chr5 180915260 25616498 0.1415939042400293 0.5566763888806127 chr6 171115067 25472860 0.14886392207648202 1.0720231306743995 chr7 159138663 30502158 0.19167031709949706 1.80115196572997 chr8 146364022 29948757 0.204618297521231 0.8780985152027357 chr9 141213431 18445559 0.13062184573647248 1.8159020041630396 chr10 135534747 20732475 0.15296796916587005 2.9721305228529626 chr11 135006516 29211386 0.21637019356902745 1.8552673482538116 chr12 133851895 24599347 0.1837803416978146 0.6530314035889766 chr13 115169878 12383471 0.10752352277389753 0.456161861742229 chr14 107349540 12919364 0.12034857345452994 0.5574246036513331 chr15 102531392 12357952 0.12052847190448755 0.5111548603407678 chr16 90354753 13123804 0.1452475222858503 1.6168608077171305 chr17 81195210 11518242 0.14185863919805122 1.5778027234275593 chr18 78077248 11485566 0.14710515923921907 1.8327113085107367 chr19 59128983 7905359 0.1336968538762116 0.9582910687380222 chr20 63025520 13209919 0.20959635081154426 0.7649483409121912 chr21 48129895 3252108 0.06756939735688183 0.486282369137651 chr22 51304566 4697810 0.09156709365790172 0.4718060824167824 chrMT 16571 163149 9.845452899643956 6.117212138064754 chrX 155270560 27660367 0.17814302337803123 0.9149225960902496 chrY 59373566 993931 0.016740294830868 0.9211947399066841