BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046438.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 4,821,352 number of mapped reads = 4,783,124 (99.21%) number of supplementary alignments = 38,589 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,392,891 number of mapped paired reads (second in pair) = 2,390,233 number of mapped paired reads (both in pair) = 4,761,930 number of mapped paired reads (singletons) = 21,194 number of mapped bases = 444,081,203 bp number of sequenced bases = 443,898,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,533,538 duplication rate = 32.65% >>>>>>> Insert size mean insert size = 20,533.354 std insert size = 1,416,052.6424 median insert size = 115 >>>>>>> Mapping quality mean mapping quality = 51.3403 >>>>>>> ACTG content number of A's = 127,080,222 bp (28.63%) number of C's = 95,365,384 bp (21.48%) number of T's = 125,036,846 bp (28.17%) number of G's = 96,378,151 bp (21.71%) number of N's = 38,285 bp (0.01%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,693,314 number of insertions = 48,220 mapped reads with insertion percentage = 0.99% number of deletions = 58,315 mapped reads with deletion percentage = 1.17% homopolymer indels = 48.01% >>>>>>> Coverage mean coverageData = 0.1435X std coverageData = 24.3573X There is a 1.55% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% 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 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 57363037 0.230142002334269 27.009049271917526 chr2 243199373 35179904 0.14465458346391377 21.4160220330304 chr3 198022430 82848110 0.41837740300429604 53.615684410911264 chr4 191154276 8544443 0.044699198881640506 1.8903125595876946 chr5 180915260 15972801 0.08828885412982852 11.193053494334405 chr6 171115067 68260218 0.3989141295196407 45.16926224351233 chr7 159138663 9460325 0.05944705593008533 7.8221204908948385 chr8 146364022 12155830 0.08305203583432547 8.507458009050417 chr9 141213431 7572808 0.053626683711126596 6.36993871641391 chr10 135534747 13531614 0.09983870778170265 15.198444172890174 chr11 135006516 9023091 0.06683448523329051 3.614926720604474 chr12 133851895 6788520 0.05071665216245164 1.5927954404420126 chr13 115169878 20576490 0.17866208037487025 23.397549488471704 chr14 107349540 6832665 0.0636487589979426 2.6538665270233115 chr15 102531392 10577831 0.10316675501684401 12.259511927071804 chr16 90354753 45683953 0.5056065285242936 70.70427470892406 chr17 81195210 5355658 0.06596027031643861 2.502888107724372 chr18 78077248 3658574 0.04685838824647098 2.0719033088643486 chr19 59128983 9504581 0.1607431840997502 11.559312528857768 chr20 63025520 4684144 0.07432138600363788 4.5991427137233725 chr21 48129895 1593813 0.03311482395712685 3.3017380696401375 chr22 51304566 2329671 0.04540864842322222 2.108166091809168 chrMT 16571 790750 47.71890652344457 17.339797378598806 chrX 155270560 5580532 0.03594069603407111 1.1985401777789693 chrY 59373566 211840 0.0035679177497945805 0.16938851653508208