BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695919.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 106,940,708 number of mapped reads = 106,290,261 (99.39%) number of supplementary alignments = 1,361,499 (1.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,305,103 number of mapped paired reads (second in pair) = 52,985,158 number of mapped paired reads (both in pair) = 105,844,242 number of mapped paired reads (singletons) = 446,019 number of mapped bases = 10,547,691,018 bp number of sequenced bases = 10,545,325,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,089,603 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 82,096.4664 std insert size = 2,735,353.7595 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.8501 >>>>>>> ACTG content number of A's = 3,131,999,626 bp (29.7%) number of C's = 2,110,579,616 bp (20.01%) number of T's = 3,112,071,958 bp (29.51%) number of G's = 2,176,036,064 bp (20.64%) number of N's = 14,638,419 bp (0.14%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 68,748,201 number of insertions = 1,055,608 mapped reads with insertion percentage = 0.98% number of deletions = 1,022,878 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 3.4072X std coverageData = 4.526X There is a 80.96% of reference with a coverageData >= 1X There is a 65.98% of reference with a coverageData >= 2X There is a 51.06% of reference with a coverageData >= 3X There is a 38.2% of reference with a coverageData >= 4X There is a 27.99% of reference with a coverageData >= 5X There is a 20.27% of reference with a coverageData >= 6X There is a 14.59% of reference with a coverageData >= 7X There is a 10.5% of reference with a coverageData >= 8X There is a 7.56% of reference with a coverageData >= 9X There is a 5.47% of reference with a coverageData >= 10X There is a 3.97% of reference with a coverageData >= 11X There is a 2.91% of reference with a coverageData >= 12X There is a 2.14% of reference with a coverageData >= 13X There is a 1.59% of reference with a coverageData >= 14X There is a 1.19% of reference with a coverageData >= 15X There is a 0.9% of reference with a coverageData >= 16X There is a 0.69% of reference with a coverageData >= 17X There is a 0.53% of reference with a coverageData >= 18X There is a 0.41% of reference with a coverageData >= 19X There is a 0.33% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 869062309 3.486700677066718 4.669096277083247 chr2 243199373 936923031 3.8524895004560724 5.241142560346332 chr3 198022430 760979389 3.8428949134701558 3.491114960055112 chr4 191154276 771111554 4.033974913540517 4.462139105701674 chr5 180915260 661271778 3.655146492341221 3.3242770474207157 chr6 171115067 695924552 4.066997513433461 4.094629801041062 chr7 159138663 530474186 3.3334085884584814 3.425783682716412 chr8 146364022 483016426 3.300103532273799 3.246800868049795 chr9 141213431 445948849 3.1579775793422935 4.091932835737927 chr10 135534747 501465912 3.699906651982019 5.085500473597574 chr11 135006516 535411512 3.965819783098469 3.9549642009369728 chr12 133851895 515631609 3.852254829862513 3.7151034584542697 chr13 115169878 368287333 3.197774794899062 3.4886479261319696 chr14 107349540 317966938 2.961977647971291 3.410391361890389 chr15 102531392 329426998 3.21293792636698 3.7031516864800587 chr16 90354753 259584551 2.872948487834392 5.141426454419349 chr17 81195210 239497313 2.949648298218577 4.019043149823645 chr18 78077248 293976746 3.765203737713706 4.853372942153783 chr19 59128983 143136653 2.42075283114543 3.473557962792669 chr20 63025520 185051609 2.936137758165264 3.5504704310343818 chr21 48129895 142324999 2.9571017971262976 6.05352926135238 chr22 51304566 104180547 2.030629145171991 3.129551336923381 chrMT 16571 12550414 757.3721561764528 203.63173499886514 chrX 155270560 377631065 2.432084131080612 2.6622200941284175 chrY 59373566 66854745 1.1260018473540903 4.750677839452373