BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926950.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,505,664 number of mapped reads = 12,240,231 (97.88%) number of supplementary alignments = 296,300 (2.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,112,993 number of mapped paired reads (second in pair) = 6,127,238 number of mapped paired reads (both in pair) = 12,073,526 number of mapped paired reads (singletons) = 166,705 number of mapped bases = 1,137,391,521 bp number of sequenced bases = 1,136,559,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 640,104 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 241,617.2074 std insert size = 4,895,476.0281 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 52.9 >>>>>>> ACTG content number of A's = 321,396,775 bp (28.28%) number of C's = 229,530,054 bp (20.2%) number of T's = 326,664,224 bp (28.74%) number of G's = 258,923,539 bp (22.78%) number of N's = 45,152 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 10,507,214 number of insertions = 188,082 mapped reads with insertion percentage = 1.51% number of deletions = 569,243 mapped reads with deletion percentage = 4.53% homopolymer indels = 52.07% >>>>>>> Coverage mean coverageData = 0.3674X std coverageData = 1.531X There is a 20.71% of reference with a coverageData >= 1X There is a 8.45% of reference with a coverageData >= 2X There is a 3.49% of reference with a coverageData >= 3X There is a 1.63% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% 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 0.01% 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 0.01% 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% 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 90804829 0.3643113450858764 1.9813470993788043 chr2 243199373 100482991 0.41317125846372965 2.9077217081757483 chr3 198022430 73645295 0.37190380402866485 0.9255300754221171 chr4 191154276 63629554 0.33287015771491296 1.083893582338572 chr5 180915260 69353393 0.38334739148040914 0.9325204734830465 chr6 171115067 64426239 0.3765082767375476 1.043027026170809 chr7 159138663 59222301 0.37214275829375293 1.0561168028200176 chr8 146364022 54738411 0.373988158100766 0.9916290034678008 chr9 141213431 51127885 0.36206106344091304 1.7714661341215923 chr10 135534747 56627254 0.41780617334977577 2.1811332060808133 chr11 135006516 54251903 0.4018465523545545 1.6201298963815451 chr12 133851895 50950844 0.3806508977702557 0.9802044995015325 chr13 115169878 31834662 0.2764148278423982 0.7790537174756728 chr14 107349540 34752382 0.323731075140145 0.8763064111552711 chr15 102531392 37040426 0.3612593692281092 0.9379198520032964 chr16 90354753 37654343 0.41673892905224363 1.7786362896629828 chr17 81195210 33962143 0.4182776668722207 1.118738002322497 chr18 78077248 30383781 0.389150255398346 1.6590768673445773 chr19 59128983 23057457 0.38995186167839213 1.4566520392568802 chr20 63025520 29824717 0.47321651610331816 1.1479392045044263 chr21 48129895 13950042 0.28984152157406534 1.0805936311243265 chr22 51304566 16219122 0.3161340844399697 0.9049390497021811 chrMT 16571 1472844 88.88081588316939 73.46103799412653 chrX 155270560 55589167 0.358014854844344 0.9989100738307208 chrY 59373566 2389536 0.04024578884145177 0.9669547919286124