BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777257.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 6,248,054 number of mapped reads = 6,123,074 (98%) number of supplementary alignments = 182,510 (2.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,075,135 number of mapped paired reads (second in pair) = 3,047,939 number of mapped paired reads (both in pair) = 6,084,622 number of mapped paired reads (singletons) = 38,452 number of mapped bases = 603,258,017 bp number of sequenced bases = 603,100,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 384,545 duplication rate = 4.71% >>>>>>> Insert size mean insert size = 104,394.553 std insert size = 3,122,721.7469 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 53.1715 >>>>>>> ACTG content number of A's = 178,662,676 bp (29.62%) number of C's = 123,570,162 bp (20.49%) number of T's = 175,488,899 bp (29.1%) number of G's = 125,323,422 bp (20.78%) number of N's = 54,855 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,787,013 number of insertions = 147,732 mapped reads with insertion percentage = 2.37% number of deletions = 68,797 mapped reads with deletion percentage = 1.1% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 0.1949X std coverageData = 1.861X There is a 12.47% of reference with a coverageData >= 1X There is a 4.52% of reference with a coverageData >= 2X There is a 1.23% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% 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 0.01% 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% 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 51339842 0.2059767867138032 4.61106794174672 chr2 243199373 59616399 0.24513385155807946 1.3481409565002724 chr3 198022430 39564336 0.19979724519086045 0.6650321681331542 chr4 191154276 36837437 0.19271050468156936 0.8365441569856487 chr5 180915260 39656830 0.21920113317140855 0.6269093789862783 chr6 171115067 28469492 0.16637630162632025 0.8075613975082684 chr7 159138663 41420797 0.26028116749981745 1.6656262150348062 chr8 146364022 29440044 0.20114262779687758 0.9617842270929206 chr9 141213431 21832363 0.15460542843123753 1.8000903118383915 chr10 135534747 29567634 0.21815537826620948 3.4072963264994733 chr11 135006516 35099563 0.25998421439154834 1.0700479914260612 chr12 133851895 27384204 0.20458585214650865 0.6054306636317413 chr13 115169878 25148193 0.21835738160632592 0.6229332977315171 chr14 107349540 11736629 0.10933096685835822 0.4529453428601141 chr15 102531392 21188499 0.20665377292449127 0.6144142788954452 chr16 90354753 17342268 0.1919353152346064 1.7164783521240972 chr17 81195210 14254863 0.17556285647884895 0.8901935751083865 chr18 78077248 13178616 0.16878945323482714 1.976594410955108 chr19 59128983 11466235 0.1939190295222903 2.4152279309751856 chr20 63025520 15195408 0.2410992880344343 0.6839482494850743 chr21 48129895 5420747 0.11262744288139419 0.549299690332524 chr22 51304566 4564482 0.08896833860752276 0.400758649743742 chrMT 16571 2833878 171.01430209401968 43.74155848805917 chrX 155270560 19491508 0.12553254139097586 0.5899801234776448 chrY 59373566 1207750 0.02034154391198265 0.9206862436981563