BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818870.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 = 2,497,043 number of mapped reads = 2,454,565 (98.3%) number of supplementary alignments = 41,314 (1.65%) number of secondary alignments = 0 number of mapped bases = 227,191,704 bp number of sequenced bases = 227,048,616 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 765,684 duplication rate = 27.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4418 >>>>>>> ACTG content number of A's = 64,605,527 bp (28.45%) number of C's = 50,240,173 bp (22.13%) number of T's = 65,469,118 bp (28.83%) number of G's = 46,730,526 bp (20.58%) number of N's = 3,272 bp (0%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,375,730 number of insertions = 29,069 mapped reads with insertion percentage = 1.14% number of deletions = 73,878 mapped reads with deletion percentage = 2.93% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0734X std coverageData = 0.7883X There is a 4.34% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 21545579 0.08644142555616742 1.1481156582264542 chr2 243199373 17251294 0.07093477991820316 1.132068662856618 chr3 198022430 14284406 0.07213529295645953 0.409083723602813 chr4 191154276 11496024 0.06014003055835382 0.4874902798157434 chr5 180915260 10026059 0.0554185368332113 0.3810010079484717 chr6 171115067 11506106 0.06724192206873285 0.4404085162781266 chr7 159138663 20365629 0.12797411148288962 1.5802464611322993 chr8 146364022 19889255 0.13588896183790303 0.7326294958056657 chr9 141213431 8481211 0.06005952082560759 0.6748669086074386 chr10 135534747 10636251 0.07847619326725123 1.1013616760575273 chr11 135006516 10133903 0.0750623251399214 0.5084029626887329 chr12 133851895 8919994 0.06664077486538386 0.3963496184461469 chr13 115169878 7007250 0.060842731812219164 0.3711939893152642 chr14 107349540 6733270 0.06272285843050655 0.42187831136482645 chr15 102531392 6330148 0.061738633178802446 0.3781727988769599 chr16 90354753 5661174 0.06265496625285445 0.8617737430985721 chr17 81195210 6167571 0.075959788760938 0.5229994421517602 chr18 78077248 4387931 0.05619986759779238 0.7563002469292254 chr19 59128983 3592916 0.06076404189126676 1.0286527754021157 chr20 63025520 7932771 0.12586601427485247 0.5841836299896175 chr21 48129895 2236103 0.046459752301558105 0.4052450913477244 chr22 51304566 2084412 0.04062819671839735 0.35149833625024696 chrMT 16571 423163 25.53635869893187 15.177706924624871 chrX 155270560 9300290 0.059897317302133775 0.4440662800132887 chrY 59373566 798994 0.013457066062024976 0.9688013582144358