BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818794.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,152,292 number of mapped reads = 3,075,726 (97.57%) number of supplementary alignments = 22,424 (0.71%) number of secondary alignments = 0 number of mapped bases = 209,192,514 bp number of sequenced bases = 209,103,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,539,699 duplication rate = 42.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4846 >>>>>>> ACTG content number of A's = 60,476,618 bp (28.92%) number of C's = 42,378,948 bp (20.27%) number of T's = 59,368,374 bp (28.39%) number of G's = 46,867,143 bp (22.41%) number of N's = 12,847 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,072,220 number of insertions = 28,281 mapped reads with insertion percentage = 0.91% number of deletions = 54,663 mapped reads with deletion percentage = 1.76% homopolymer indels = 39.38% >>>>>>> Coverage mean coverageData = 0.0676X std coverageData = 0.8057X There is a 2.83% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% 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 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 17153173 0.06881897798762154 1.2816856697637755 chr2 243199373 18576131 0.07638231452183884 1.3140045482446132 chr3 198022430 14406950 0.07275413194353791 0.5333159655167673 chr4 191154276 13858080 0.07249683496486367 0.6379303315507264 chr5 180915260 13071911 0.07225433056338089 0.5494669660233704 chr6 171115067 12245454 0.0715626871127602 0.6228992793334007 chr7 159138663 11094251 0.06971436601801788 0.6933731300696871 chr8 146364022 10975324 0.07498648814119087 0.6522886653499705 chr9 141213431 8939293 0.06330341906358751 0.6504540301183286 chr10 135534747 9786622 0.07220747606515988 0.8300545491169712 chr11 135006516 10043334 0.07439147603808989 0.6347719569434356 chr12 133851895 9632987 0.07196750557771334 0.5731939200359443 chr13 115169878 6721362 0.05836041608032267 0.478557796397274 chr14 107349540 6535582 0.060881322826348394 0.5912647335163649 chr15 102531392 5927810 0.05781458619034451 0.47944160572207145 chr16 90354753 6321260 0.06996045908066396 0.9145147001023363 chr17 81195210 5641938 0.06948609406884963 0.5757966775232852 chr18 78077248 5752678 0.07367931308234635 0.8982316908021272 chr19 59128983 4300938 0.07273823735476728 1.0997043729961122 chr20 63025520 4650942 0.0737945835274346 0.5843013174761481 chr21 48129895 2879521 0.05982811722319361 0.5272096123738232 chr22 51304566 2565450 0.05000432125281013 0.5059516304668117 chrMT 16571 15639 0.9437571661336069 2.017448204786639 chrX 155270560 6124712 0.039445417083573346 0.5114170814399173 chrY 59373566 1971172 0.0331994881358482 1.4280394403490058