BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081257.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 = 3,022,475 number of mapped reads = 2,565,086 (84.87%) number of supplementary alignments = 19,767 (0.65%) number of secondary alignments = 0 number of mapped bases = 172,094,995 bp number of sequenced bases = 172,018,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,486 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4834 >>>>>>> ACTG content number of A's = 47,329,697 bp (27.51%) number of C's = 31,116,072 bp (18.09%) number of T's = 55,353,128 bp (32.18%) number of G's = 38,176,802 bp (22.19%) number of N's = 42,982 bp (0.02%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,477,743 number of insertions = 14,184 mapped reads with insertion percentage = 0.55% number of deletions = 45,430 mapped reads with deletion percentage = 1.75% homopolymer indels = 49.77% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.4816X There is a 4.75% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 19394441 0.0778110037286527 1.0745124951301932 chr2 243199373 10932661 0.04495349171808926 0.419411077543739 chr3 198022430 12004923 0.060624056577833124 0.28766287704697946 chr4 191154276 7736405 0.04047204782382163 0.24779938789476744 chr5 180915260 11021927 0.06092314711318437 0.27921740601580025 chr6 171115067 11263725 0.06582544247842301 0.35715744436080366 chr7 159138663 10615555 0.06670632264894673 0.5260589345192073 chr8 146364022 10454552 0.07142842795068859 0.657392619474334 chr9 141213431 5235843 0.03707751424862696 0.3507297425640993 chr10 135534747 5567147 0.04107542252615117 0.5187602455048933 chr11 135006516 8809528 0.06525261343682108 0.46631809490044235 chr12 133851895 5394126 0.040299212797846456 0.23080905190017917 chr13 115169878 5078174 0.044092900749621355 0.23436132956922565 chr14 107349540 6836207 0.06368175401589983 0.2996619229161924 chr15 102531392 3330603 0.032483739223983225 0.20190149563722432 chr16 90354753 5381513 0.05955982193875291 0.2977534048153885 chr17 81195210 3073657 0.03785515180021087 0.2760399059540739 chr18 78077248 3902305 0.0499800530879367 0.5858077708812172 chr19 59128983 4638701 0.07845054598689782 0.7270750969524796 chr20 63025520 4452096 0.07063957584165906 0.30641248015833294 chr21 48129895 2922857 0.06072851395167182 0.298630036914019 chr22 51304566 1160175 0.022613484343674207 0.16587393964881356 chrMT 16571 13272 0.8009172651016837 0.9693332281011452 chrX 155270560 12407269 0.07990741451566864 0.3543596383842443 chrY 59373566 467333 0.007871061677514873 0.15538424820307323