BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926946.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 = 12,032,546 number of mapped reads = 11,794,230 (98.02%) number of supplementary alignments = 247,274 (2.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,918,809 number of mapped paired reads (second in pair) = 5,875,421 number of mapped paired reads (both in pair) = 11,648,688 number of mapped paired reads (singletons) = 145,542 number of mapped bases = 1,076,018,550 bp number of sequenced bases = 1,075,218,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 687,588 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 229,829.9871 std insert size = 4,722,154.9922 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.1563 >>>>>>> ACTG content number of A's = 308,373,879 bp (28.68%) number of C's = 207,049,127 bp (19.26%) number of T's = 314,082,137 bp (29.21%) number of G's = 245,498,603 bp (22.83%) number of N's = 214,604 bp (0.02%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 9,554,371 number of insertions = 176,575 mapped reads with insertion percentage = 1.47% number of deletions = 550,468 mapped reads with deletion percentage = 4.55% homopolymer indels = 52.47% >>>>>>> Coverage mean coverageData = 0.3476X std coverageData = 1.5677X There is a 20.12% of reference with a coverageData >= 1X There is a 7.92% of reference with a coverageData >= 2X There is a 3.22% of reference with a coverageData >= 3X There is a 1.46% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% 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 0.02% 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 0.01% 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% 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 96180621 0.38587916296505437 1.955687678535515 chr2 243199373 96826406 0.3981359195362728 2.6637056948650413 chr3 198022430 60162468 0.303816431300232 0.8066480162449414 chr4 191154276 69934721 0.3658548606048446 1.1511406616127846 chr5 180915260 72316071 0.3997234451090527 0.9350153686455579 chr6 171115067 64203863 0.375208706782086 1.0407624681947714 chr7 159138663 53379810 0.3354295492604459 1.0917355465374434 chr8 146364022 59977197 0.40978101162046504 1.0885956386892168 chr9 141213431 36324512 0.25723128276658047 1.4999421307413465 chr10 135534747 57380796 0.42336594319979065 3.378015518856078 chr11 135006516 55519939 0.41123895827368806 1.7944079188041717 chr12 133851895 51884181 0.38762380614783226 0.946132467434431 chr13 115169878 35951153 0.3121576025286751 0.8260398697554924 chr14 107349540 26606044 0.2478449744637937 0.7427683190429109 chr15 102531392 24867923 0.2425396019201612 0.7234036951393196 chr16 90354753 35030355 0.3876979775485635 2.0786550665510783 chr17 81195210 27036381 0.3329799996822473 1.2013773048465102 chr18 78077248 31405707 0.40223890831808007 1.5870797631737898 chr19 59128983 16042999 0.2713220858204174 1.4814136135268146 chr20 63025520 13619322 0.2160921798027212 0.7035358684520661 chr21 48129895 11551951 0.24001612719080315 1.1186879906015545 chr22 51304566 11537323 0.2248790682685046 0.7510393252498536 chrMT 16571 84461 5.096916299559472 4.983745398198415 chrX 155270560 66418183 0.42775773462786504 1.0834645823289744 chrY 59373566 1776163 0.029915046706138555 1.1245372024426032